Changeset 6142 for branches/stable_5.0

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Timestamp:
15/08/09 12:21:41 (3 years ago)
Author:
westram
Message:
  • backport [6141] (parts not affecting code at all, i.e. helpfiles, figs, ..)
Location:
branches/stable_5.0
Files:
148 modified

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  • branches/stable_5.0/ARBDB/Synchronized_Alignments.txt

    r5390 r6142  
     1 
     2 *** This is just a draft, it's not implemented *** 
     3 
    14 
    25        Automatic synchronization of DNA- and Protein-Alignments 
    … …  
    1821        sync_flag-value         meaning 
    1922        -------------------------------------------------------------------------------- 
    20         SYNC_NOT                species should not be syncronized (this is the default 
     23        SYNC_NOT                species should not be synchronized (this is the default 
    2124                                value in case of missing sync_flag). 
    2225 
    … …  
    2831 
    2932 
    30   * If /species_data/species_xxx/ali_dna does not exist no syncronization will be done 
     33  * If /species_data/species_xxx/ali_dna does not exist no synchronization will be done 
    3134    for this species!! 
    3235 
    33 - Changed read/write-machanism for synced alignments (this affects only .../ali_xx/data): 
     36- Changed read/write-mechanism for synchronized alignments (this affects only .../ali_xx/data): 
    3437 
    3538  * reading ali_dna/data:       if sync_flag==SYNC_DNA => re-align; 

  • branches/stable_5.0/Doxyfile

    r2529 r6142  
    160160SKIP_FUNCTION_MACROS   = YES 
    161161#--------------------------------------------------------------------------- 
    162 # Configuration::addtions related to external references    
     162# Configuration::additions related to external references    
    163163#--------------------------------------------------------------------------- 
    164164TAGFILES               =  
    … …  
    187187DOT_CLEANUP            = YES 
    188188#--------------------------------------------------------------------------- 
    189 # Configuration::addtions related to the search engine    
     189# Configuration::additions related to the search engine    
    190190#--------------------------------------------------------------------------- 
    191191SEARCHENGINE           = NO 

  • branches/stable_5.0/GDE/CLUSTALW/clustalw_help

    r1754 r6142  
    197197or sequences.  This is done progressively, following the branching order in  
    198198the GUIDE TREE.  The basic parameters to control this are two gap penalties and 
    199 the scores for various identical-non-indentical residues.   
     199the scores for various identical-non-identical residues.   
    200200 
    2012011) and 2) The GAP PENALTIES are set by menu items 1 and 2. These control the  

  • branches/stable_5.0/GDEHELP/HELP_PLAIN/CAP2.help

    r2248 r6142  
    156156 
    157157   Slight modifications by S. Smith on Mon Feb 17 10:18:34 EST 1992. 
    158    These changes allow for command line arguements for several 
     158   These changes allow for command line arguments for several 
    159159   of the hard coded parameters, as well as a slight modification to 
    160160   the output routine to support GDE format.  Changes are commented 

  • branches/stable_5.0/HELP_SOURCE/Makefile

    r5892 r6142  
    114114$(XML_LOCATION)/%.xml : $(HLP_SOURCE)/%.hlp $(DTD) 
    115115                @test \! -f $(HLP_GENERATED)/$(<F) || \ 
    116                                 ( echo $<:1: exists twice -- only one existance allowed; \ 
     116                                ( echo $<:1: exists twice -- only one existence allowed; \ 
    117117                                  echo $(HLP_GENERATED)/$(<F):1: other occurrence \ 
    118118                                  && false ) 
    … …  
    122122$(XML_LOCATION)/%.xml : $(HLP_GENERATED)/%.hlp $(DTD) 
    123123                @test \! -f $(HLP_SOURCE)/$(<F) || \ 
    124                                 ( echo $<:1: exists twice -- only one existance allowed; \ 
     124                                ( echo $<:1: exists twice -- only one existence allowed; \ 
    125125                                  echo $(HLP_SOURCE)/$(<F):1: other occurrence \ 
    126126                                  && false ) 

  • branches/stable_5.0/HELP_SOURCE/arb_help2xml.cxx

    r6132 r6142  
    10881088    link.add_attribute("source_line", source_line); 
    10891089 
    1090     if (type&(LT_HLP|LT_PDF|LT_PS)) {               // other links (www, email) cannot be checked for existance here 
     1090    if (type&(LT_HLP|LT_PDF|LT_PS)) {               // other links (www, email) cannot be checked for existence here 
    10911091        string fullhelp = ((type&LT_HLP) ? locate_helpfile : locate_document)(dest); 
    10921092        if (fullhelp.empty()) { 
    … …  
    12661266                            } 
    12671267                            catch (string& err) { 
    1268                                 ; // ingore duplicated link in text 
     1268                                ; // ignore duplicated link in text 
    12691269                            } 
    12701270                            auto_references.push_back(Link(link_target, sec.StartLineno())); 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/FAQS.hlp

    r2986 r6142  
    3131 
    3232 
    33 QUESTION Finally, do you have a 23S alignment, that I could use? I have tryed to 
     33QUESTION Finally, do you have a 23S alignment, that I could use? I have tried to 
    3434         build my own, based on the sequences available from RDP. But that's only 34 
    3535         sequences, and when I align my own 23S sequences against those, the computer 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/Protection.hlp

    r2986 r6142  
    1515DESCRIPTION     An individual protection level (0 - 6) can be assigned to 
    1616                all types of database entries (sequences and additional 
    17                 information stored in the paticular 'field').  
     17                information stored in the particular 'field').  
    1818                To modify any entries, a protection level has to be selected 
    1919                from the 'Protection' menu of the main window equal or higher 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/ap_stack.hlp

    r2986 r6142  
    2626                will be discarded. 
    2727 
    28 NOTES           The initial tree will be stored at program startup. 
     28NOTES           The initial tree will be stored at program start-up. 
    2929 
    3030                When you restore the last tree from the tree stack it will be stored again automatically, 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb.hlp

    r5711 r6142  
    108108 
    109109                Up to six hierarchical protection levels can be individually 
    110                 asigned to database entries to prevent unintended modification 
     110                assigned to database entries to prevent unintended modification 
    111111                or loss of data. 
    112112 
    … …  
    121121                ARB tools and integrated foreign software (PHYLIP [4], DE SOETE 
    122122                [1], fastDNAml [4]) allow calculation of similarity/distance 
    123                 matrices, conservation profiles, selection masks and phylogentic 
     123                matrices, conservation profiles, selection masks and phylogenetic 
    124124                tree reconstruction using different treeing approaches. 
    125125 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_db.hlp

    r2986 r6142  
    8484                        [gene_data]             // container containing genes 
    8585 
    86         extended::=                             // analoguous to species 
    87  
    88         gene::=                                 // analoguous to species 
     86        extended::=                             // analogous to species 
     87 
     88        gene::=                                 // analogous to species 
    8989 
    9090        ali_xxx::=      'data'                  // the sequence 
    … …  
    9797        alignment::=    'alignment_name'        // name of the alignment (prefix 'ali_') 
    9898                        'alignment_len'         // length of longest sequence 
    99                         'alignment_write_security' // default write sequerity 
     99                        'alignment_write_security' // default write security 
    100100                        'alignment_type'        // dna or pro 
    101101                        'aligned'               // ==1 when all sequences have the same 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_edit.hlp

    r4947 r6142  
    3333                species' (see LINK{glossary.hlp}) and 'SAI' (sequence associated 
    3434                information) data stored in the data base, and to insert 
    35                 new data. Potential scondary structure is automatically checked 
     35                new data. Potential secondary structure is automatically checked 
    3636                and the information can be displayed with the primary structure. 
    3737                Protection levels can be assigned to the sequences and 'SAI' 
    … …  
    4343                ARB tools are exported to the editor every 5 seconds. 
    4444 
    45                 Multiple editors can be used synchronuously. 
     45                Multiple editors can be used synchronously. 
    4646 
    4747 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_edit4.hlp

    r2531 r6142  
    2929    Alternatively: 
    3030 
    31         to load marked, all SAI's as well as seqeunces from 
     31        to load marked, all SAI's as well as sequences from 
    3232        a number of closest relatives as they are arranged and grouped in 
    3333        the tree visualized in the ARB_NT main window select "Edit Marked 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_gde.hlp

    r2986 r6142  
    1919 
    2020WARNINGS        Some of the GDE tools are not available or do not run properly 
    21                 blast/fasta require proberly installed databases 
     21                blast/fasta require properly installed databases 
    2222 
    2323BUGS            No bugs known 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_intro.hlp

    r5775 r6142  
    4141                ARB databases stored in any directory with read and write 
    4242                permission can be opened starting 'arb' from the current 
    43                 directory. Find the path by sucessively selecting the 
     43                directory. Find the path by successively selecting the 
    4444                corresponding directories from the 'Existing Files and 
    4545                Directories' subwindow. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_pars.hlp

    r2986 r6142  
    6060 
    6161                                Add all marked species to this tree. 
    62                                 No local rearangements are performed. 
     62                                No local rearrangements are performed. 
    6363                                If the species are already in the tree do 
    6464                                nothing. 
    … …  
    7575                        Tree/add marked species: 
    7676 
    77                                 Quick add plus local rearangements. 
     77                                Quick add plus local rearrangements. 
    7878 
    7979                        Tree/add selected species: 
    8080 
    81                                 Quick add sel. species plus local rearangements. 
     81                                Quick add sel. species plus local rearrangements. 
    8282 
    8383                        Tree/Optimization/Local 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/arb_pars_init.hlp

    r2986 r6142  
    2323                you only get a new window (with some action buttons).    
    2424 
    25 WARNINGS        You can only change filter settings at startup time. 
     25WARNINGS        You can only change filter settings at start-up time. 
    2626                You should use filters in combination with large databases 
    2727                to speed up computation. 
    … …  
    3030                '.'. 
    3131 
    32 BUGS            All sequences are read at startup time.  Sequence changes 
     32BUGS            All sequences are read at start-up time.  Sequence changes 
    3333                afterwards are ignored.  Restart arb_parsimony if you want 
    3434                them to take effect. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/awt_csp.hlp

    r2986 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile strunk******** 
    11 TITLE           Estimate Parameters from Coloumn Statistics 
     11TITLE           Estimate Parameters from Column Statistics 
    1212 
    1313OCCURRENCE      ARB_DIST 
    1414 
    15 DESCRIPTION     In a standart RNA, base frequencies are not equally 
     15DESCRIPTION     In a standard RNA, base frequencies are not equally 
    1616                distributed. Especially in the archea subclass we find 
    1717                extremely G+C rich sequences. 
    … …  
    2626                parts have a significant higher G+C content than non 
    2727                helical parts. 
    28                 One strait forward algorhythm would calculate each frequency 
    29                 independently for each coloumn. 
     28                One strait forward algorithm would calculate each frequency 
     29                independently for each column. 
    3030                Especially for small datasets the resulting frequencies would 
    3131                look like random data, as too few examples are analyzed. 
    … …  
    3333                In ARB we implemented a combination of the 2 approaches. 
    3434                        Lets say we want to estimate a Parameter 'P' with 
    35                         a maximum variance 'maxvar', so we need a minumum 
     35                        a maximum variance 'maxvar', so we need a minimum 
    3636                        samples 'minsap'. 
    3737 
    … …  
    4545                          minimum of independent events. 
    4646 
    47                         - The final parameter estimate for a coloumn is a 
     47                        - The final parameter estimate for a column is a 
    4848                          weighted sum between the estimate for the 
    4949                          cluster and the estimate for the single position. 
    5050 
    51                 You can give your favourite method a higher weight by 
    52                 controlling the smothing parameter: 
     51                You can give your favorite method a higher weight by 
     52                controlling the smoothing parameter: 
    5353 
    5454                        Less smoothing -> independent parameter estimates 
    … …  
    7171 
    7272                         1. Much smoothing of parameters is selected and 
    73                          2. your are anlazing ribosomal RNA and 
     73                         2. you are analyzing ribosomal RNA and 
    7474                         3. 'Use Helix Information' is turned off 
    7575 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/check_quality.hlp

    r2986 r6142  
    1313OCCURRENCE      ARB_NT 
    1414 
    15 DESCRIPTION     Takes sequences, a tree and a coloumn statistic as input, 
     15DESCRIPTION     Takes sequences, a tree and a column statistic as input, 
    1616                and generates a short sequence quality output string, which 
    1717                will be stored into the database under a user defined key. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/checkgcg.hlp

    r2986 r6142  
    1313OCCURRENCE      ARB_NT/ETC/Check GCG List 
    1414 
    15 DESCRIPTION     !!!!!  Currenlty no help available !!!!!! 
     15DESCRIPTION     !!!!!  Currently no help available !!!!!! 
    1616 
    1717NOTES           None     

  • branches/stable_5.0/HELP_SOURCE/oldhelp/commands.hlp

    r5726 r6142  
    191191                extract_words("chars",val) 
    192192 
    193                     Search for all words (seperated by ',' ';' ':' ' ' or 'tab') that 
     193                    Search for all words (separated by ',' ';' ':' ' ' or 'tab') that 
    194194                    contain more characters of type chars than val, sort them 
    195                     alphabetically and write them seperated by ' ' to the output 
    196  
    197         STRING COMPARATION 
     195                    alphabetically and write them separated by ' ' to the output 
     196 
     197        STRING COMPARISON 
    198198 
    199199               compare(a,b)             return -1 if a<b, 0 if a=b, 1 if a>b 
    … …  
    218218                The above functions work as binary operators (see below). 
    219219 
    220                 To avoid 'devision by zero'-errors, the operators 'div', 'per_cent' and 'rest' 
     220                To avoid 'division by zero'-errors, the operators 'div', 'per_cent' and 'rest' 
    221221                return 0 if the second argument is zero. 
    222222 
    … …  
    308308 
    309309                        like extract_words, but do not sort words, but rel_len is the minimum 
    310                         percantage of characters of a word that mach a character in 'chars' 
    311                         before word is taken. All words will be seperated by white space. 
     310                        percentage of characters of a word that mach a character in 'chars' 
     311                        before word is taken. All words will be separated by white space. 
    312312 
    313313                taxonomy([treename,] depth) 
    … …  
    442442 
    443443                        In escapedCommand you have to escape '\' and '"' by 
    444                         preceeding a '\'. If you nest calls you have to use multiple escapes 
     444                        preceding a '\'. If you nest calls you have to use multiple escapes 
    445445                        (e.g. inside an export filter - which is in fact an 
    446446                        SRT expression - you'll have to use double escapes). 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/concatenate.hlp

    r4112 r6142  
    1111TITLE            CONCATENATION of ALIGNMENTS / SEQUENCES 
    1212 
    13 DESCRIPTION With the help of concatenation function, one can cancatenate the aligned sequences, which are contained in the same species preserving the ALIGNMENT.  
    14             Before using concatenation function make sure that the species contains more than two aligned or unaligned sequences.  
     13DESCRIPTION 
    1514 
    16             Specify new name for the newly created concatenated alignment in the field "New Alignment Name" (Make sure that the new alignment name starts with "ali_.....").  
     15            With the help of concatenation function, one can concatenate the aligned 
     16            sequences, which are contained in the same species preserving the ALIGNMENT. 
     17            Before using concatenation function make sure that the species contains more 
     18            than two aligned or unaligned sequences. 
    1719 
    18             Use "Sequence Type" button to load the desired type of alignments/sequences from the database.  
     20            Specify new name for the newly created concatenated alignment in the field 
     21            "New Alignment Name" (Make sure that the new alignment name starts with 
     22            "ali_....."). 
    1923 
    20             Use Arrow buttons (located in between the lists) to select or remove the alignments into/from the "Alignments to be concatenated" list.  
     24            Use "Sequence Type" button to load the desired type of alignments/sequences 
     25            from the database. 
    2126 
    22             You can also rearrange the order of concatenation of alignments by using "up" and "down" arrow keys (located by the side of "Alignments to be concatenated" list) before performing actual concatenation.  
     27            Use Arrow buttons (located in between the lists) to select or remove the 
     28            alignments into/from the "Alignments to be concatenated" list. 
    2329 
    24             Pressing CLEAR LIST button clears the alignemts list selected for concatenation.  
     30            You can also rearrange the order of concatenation of alignments by using "up" 
     31            and "down" arrow keys (located by the side of "Alignments to be concatenated" 
     32            list) before performing actual concatenation. 
    2533 
    26             Use "Alignment Separator" to specify the tag/separator between the alignments to be concatenated.  
     34            Pressing CLEAR LIST button clears the alignments list selected for 
     35            concatenation. 
    2736 
    28             Pressing CONCATENATE button performs concatenation function for the alignments selected in the order of the alignments present in the "Alignments to be concatenated" list.  
     37            Use "Alignment Separator" to specify the tag/separator between the alignments 
     38            to be concatenated. 
    2939 
    30             Use MERGE SIMILAR SPECIES button to create new species by merging similar species (for e.g., Similar species having different sequence alignments).  
    31             Additionally, you can do the same from the "Species" menu clicking on "Merge Similar Species" item. 
     40            Pressing CONCATENATE button performs concatenation function for the alignments 
     41            selected in the order of the alignments present in the "Alignments to be 
     42            concatenated" list. 
    3243 
    33             If the database contains similar species with different sequence alignments use "MERGE and CONCATENATE" button to generate new species by merging similar species in the database and concatenating the different sequence alignments contained in the newly merged species. 
     44            Use MERGE SIMILAR SPECIES button to create new species by merging similar 
     45            species (for e.g., Similar species having different sequence alignments). 
     46            Additionally, you can do the same from the "Species" menu clicking on "Merge 
     47            Similar Species" item. 
     48 
     49            If the database contains similar species with different sequence alignments 
     50            use "MERGE and CONCATENATE" button to generate new species by merging similar 
     51            species in the database and concatenating the different sequence alignments 
     52            contained in the newly merged species. 
    3453     
    35 NOTES       If problems occurs during "Merging similar species" and/or "Concatenation", try the following - 
     54NOTES 
     55 
     56            If problems occurs during "Merging similar species" and/or "Concatenation", 
     57            try the following - 
    3658         
    37             1. Search the database for the "merged_species" field and mark the listed species, if any, and delete them. 
     59            1. Search the database for the "merged_species" field and mark the listed 
     60            species, if any, and delete them. 
    3861     
    39             2. Then search the database for the <criterion_field> to use for merging similar species. Mark the resulting species and perform merging similar species.  
     62            2. Then search the database for the <criterion_field> to use for merging 
     63            similar species. Mark the resulting species and perform merging similar 
     64            species. 
    4065     
    41             3. Usually newly generated (merged) species are marked and use the same to perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT coinside with the selected alignments (names) to be concatenated !!!           
     66            3. Usually newly generated (merged) species are marked and use the same to 
     67            perform concatenation. CAUTION: Make sure that the new alignment name DOES NOT 
     68            coinside with the selected alignments (names) to be concatenated !!! 
    4269 
    4370EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/cons_params.hlp

    r2986 r6142  
    1414OCCURRENCE      ARB_NT/SAI/Consensus/expert 
    1515 
    16 DESCRIPTION     Allows to define the paramters for consensus calculation. 
     16DESCRIPTION     Allows to define the parameters for consensus calculation. 
    1717 
    1818                The left part of the 'Expert Window' is similar to the 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/consensus_def.hlp

    r5712 r6142  
    2323 
    2424                            If the switch is 'off', the algorithm will virtually remove all gaps. 
    25                             That means if you have a coloumn with two 'A's 
     25                            That means if you have a column with two 'A's 
    2626                            and 500 gaps the program thinks of 100% 'A'. 
    2727                            (If the switch is 'on', the relative number of 'A's would be 2%) 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/dist.hlp

    r3024 r6142  
    3939                4. Display the 'Select Filter' window by pressing the button 
    4040                   after the 'Filter' prompt and define an alignment- 
    41                    associated mask which defines aligment positions to 
     41                   associated mask which defines alignment positions to 
    4242                   include for treeing. 
    4343 
    … …  
    4646                6. Select rate matrix: !!! not implemented !!! 
    4747 
    48                      7. Type characters for the exclusion of aligment postions to 
     48                     7. Type characters for the exclusion of alignment postions to 
    4949                        the 'Exclude Column' subwindow. The positions are 
    5050                        excluded from the calculation of binary distance values 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/e4.hlp

    r5260 r6142  
    3939                ARB tools are exported to the editor every 5 seconds. 
    4040 
    41                 Multiple editors can be used synchronuously. 
     41                Multiple editors can be used synchronously. 
    4242 
    4343 
    … …  
    127127                        Edit-mode: 
    128128 
    129                                 Edit-mode is devided into two submodes: Insert-mode 
     129                                Edit-mode is divided into two submodes: Insert-mode 
    130130                                and Replace-mode. Toggle between these submodes 
    131131                                with the 'Insert/Replace' button on the menuboard 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/e4_block.hlp

    r2986 r6142  
    2020 
    2121 
    22                 More selection functions are availiable in the first section 
     22                More selection functions are available in the first section 
    2323                of the Block menu: 
    2424 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/e4_options.hlp

    r3669 r6142  
    1919                Online Sequence Compression (OSC) is a way to hide column positions 
    2020                (normally: column positions containing only or many gaps) in order 
    21                 to simplify editing of aligments with wide gaps. 
     21                to simplify editing of alignments with wide gaps. 
    2222 
    2323                OSC affects only the manner how sequences are DISPLAYED in the 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/e4_replace.hlp

    r5782 r6142  
    2626                 
    2727WARNINGS        There are no further questions if you press GO. 
    28                 If you pressed GO accidently, press UNDO to clean up the mess. 
     28                If you pressed GO accidentally, press UNDO to clean up the mess. 
    2929 
    3030BUGS            None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/e4_search.hlp

    r5782 r6142  
    1818 
    1919                        In the text field you can enter multiple search patterns. 
    20                         Different patterns are seperated by newlines or commas. 
     20                        Different patterns are separated by newlines or commas. 
    2121 
    2222                        '?' is treated as single letter wildcard 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/extended.hlp

    r3614 r6142  
    1212TITLE           SAI Sequence Associated Information 
    1313 
    14 DESCRIPTION     The main database devides all sequences into two groups: 
     14DESCRIPTION     The main database divides all sequences into two groups: 
    1515 
    1616                    1. Species sequences -> Species 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/gde.hlp

    r941 r6142  
    5454        sequence analysis functions into a common 
    5555        environment. The GDE takes care of the user 
    56         interface issues, and allows the programer to 
     56        interface issues, and allows the programmer to 
    5757        concentrate on the analysis itself. Existing programs 
    5858        can be tied into the GDE in a matter of hours (or 
    … …  
    7272SECTION What's New for this Release 
    7373 
    74         GDE 2.2 represents a maintainence release. Several 
     74        GDE 2.2 represents a maintenance release. Several 
    7575        small bugs have been fixed, as well as new editing 
    7676        features and user interface elements. Also, I have 
    … …  
    9090        useful "yanking" feature has been added by Scott 
    9191        Ferguson from Exxon Research, and the capability 
    92         to export the colormap for a seqeunce (see 
    93         appendicies A/C). Among the bugs fixed in this 
     92        to export the colormap for a sequence (see 
     93        appendices A/C). Among the bugs fixed in this 
    9494        release are: 
    9595 
    … …  
    111111        and can be run remotely on any system capable of 
    112112        running X Windows Release 4. You should have at 
    113         least 15 meg of free disk space available. The binay 
     113        least 15 meg of free disk space available. The binary 
    114114        release for SparcStations was compiled under 
    115115        SunOS 4.1.2 and Openwindows 3.0. 
    … …  
    369369        programs. Programs of the form: 
    370370 
    371                 program_name -a1 argument1 -a2 arguement2 -f inputfile -er errorfile > outputfile 
     371                program_name -a1 argument1 -a2 argument2 -f inputfile -er errorfile > outputfile 
    372372 
    373373        can be specified in the .GDEmenus file directly. As 
    … …  
    545545                        Minimum overlap                 Number of bases required for overlap 
    546546                        Percent match within overlap    Percentage match required in the overlap 
    547                                                         region before merge is alowwed. 
     547                                                        region before merge is allowed. 
    548548 
    549549                Comments: 
    … …  
    614614        Author: Don Gilbert 
    615615 
    616         Parameters: Many, but can easily be run in interactive mdoe. 
     616        Parameters: Many, but can easily be run in interactive mode. 
    617617 
    618618        Comments: 
    … …  
    621621                        The latest versionsupports over a dozen different file formats, as 
    622622                        well as formating capabilities for publication. GDE makes of Readseq 
    623                         for importing and exporting seqeuences as well as a filtering tool to 
     623                        for importing and exporting sequences as well as a filtering tool to 
    624624                        some external functions. 
    625625 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/gene_info.hlp

    r5768 r6142  
    110110                table, if it can reproduce them. 
    111111 
    112                 ARB_translation          if 'translation' was NOT reproducable, this 
     112                ARB_translation          if 'translation' was NOT reproducible, this 
    113113                                         contains the result of the translation. In 
    114114                                         this case the 'translation' has not been removed by ARB. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/gene_search.hlp

    r5785 r6142  
    2222 
    2323DESCRIPTION     Searches for a (set of) genes 
    24                 that match (dont match) a query or are marked. 
     24                that match (don't match) a query or are marked. 
    2525                 
    2626                The database is scanned for 'genes' which contain (or do not 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/gene_species.hlp

    r2986 r6142  
    2727                alignment(s). 
    2828 
    29 NOTES           It's possible to export these gene-species to a seperate ARB 
     29NOTES           It's possible to export these gene-species to a separate ARB 
    3030                database using the merge tool. 
    3131 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/gene_species_field_transfer.hlp

    r2986 r6142  
    2929                         no 'Source field'. 
    3030 
    31                 - Check if the example shows your intented result. 
     31                - Check if the example shows your intended result. 
    3232 
    3333NOTES           The example will be calculated for the gene-species which is selected 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/glossary.hlp

    r5775 r6142  
    6161        NDS 
    6262 
    63                         Node Display Setup: defines informatio which is displayed at 
     63                        Node Display Setup: defines information which is displayed at 
    6464                        tree nodes. 
    6565 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/helixsym.hlp

    r6124 r6142  
    2929                     The left textfield contains one or more base-pairs. Each base 
    3030                     pair contains two characters (bases, gaps-characters, ...). 
    31                      Base-pairs are seperated by spaces (' ').  
     31                     Base-pairs are separated by spaces (' ').  
    3232 
    3333                     The right textfield contains the helix symbol used for each 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/help.hlp

    r5775 r6142  
    7676 
    7777                "Menu bars" at the top of windows (if present) are used to 
    78                         expose menu choises. The menus are displayed after 
     78                        expose menu choices. The menus are displayed after 
    7979                        clicking on the prompts of the menu bar. 
    8080 
    … …  
    8585                "Menus" initiate actions after clicking on the items. 
    8686 
    87                 "Scroll bars" at the exterme right and bottom of windows and 
     87                "Scroll bars" at the extreme right and bottom of windows and 
    8888                        subwindows allow to move through the display area in 
    8989                        various increments. 
    … …  
    9898                        (see LINK{mode.hlp}) 
    9999 
    100                 "Press" means hold down the mous button while completeing an 
     100                "Press" means hold down the mouse button while completing an 
    101101                        operation. 
    102102 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/importift.hlp

    r6091 r6142  
    6060 
    6161DESCRIPTION     First of all the converter appends all import files maching 
    62                 the filepattern into one file. The files are seperated by the 
     62                the filepattern into one file. The files are separated by the 
    6363                string defined with the keyword  SEQUENCEEND. 
    6464 
    … …  
    7474                        - run commands with the concatenated lines 
    7575 
    76                    Known commands are (they are exucuted in the order listed here): 
     76                   Known commands are (they are executed in the order listed here): 
    7777 
    7878                         - SRT "SRT_STRING" 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/max_freq.hlp

    r2986 r6142  
    1515DESCRIPTION     Finds the most frequent base in each column for all marked 
    1616                species. Than the number of all sequences with this base are 
    17                 devided by: 
     17                divided by: 
    1818                        a: the number of all marked sequences, if not ignoring gaps 
    1919                        b: the number of bases in this column, if ignoring gaps 
    … …  
    3636                Ignoring Gaps will result in 7/11 == 64 % 
    3737                which is converted to '6'. 
    38                 Otherwise we get 7/16 == 44% which will be indecated by a 
     38                Otherwise we get 7/16 == 44% which will be indicated by a 
    3939                '4' in the target sequence. 
    4040 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mg_names.hlp

    r5050 r6142  
    5050                Normally merging is not allowed when there are duplicated species. 
    5151 
    52                 You may overide that behavior by checking 'Allow merging duplicates', 
     52                You may override that behavior by checking 'Allow merging duplicates', 
    5353                but be warned: 
    5454 
    5555                    It is VERY DANGEROUS to merge when duplicated species are in your 
    56                     databases, cause there is no garantee, that duplicates with the 
     56                    databases, cause there is no guarantee, that duplicates with the 
    5757                    same .NUM suffix refer to the same species. 
    5858                    You may easily overwrite or duplicate your data! 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mg_preserve.hlp

    r3045 r6142  
    4545 
    4646                When merging similar databases with many species, searching adapt candidates 
    47                 may take a loong time. Press KILL in the status window to abort the process. 
     47                may take a long time. Press KILL in the status window to abort the process. 
    4848 
    4949EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mg_spec_sel_field.hlp

    r2986 r6142  
    2727                        to corresponding field and species of db II 
    2828 
    29 NOTES           Transfering fields that are not of string type in append mode 
     29NOTES           Transferring fields that are not of string type in append mode 
    3030                does not work 
    3131 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mg_species.hlp

    r5785 r6142  
    1818                        * database searching, 
    1919                        * comparison of the two databases, 
    20                         * transfering data from left to right 
     20                        * transferring data from left to right 
    2121                        * realigning sequences to new alignment 
    2222 
    … …  
    7777                box in the upper center of the TRANSFER SPECIES window, the 
    7878                program will try to find those species in both databases, 
    79                 create a column reference list, and realign all transfered 
     79                create a column reference list, and realign all transferred 
    8080                sequences. 
    8181                To enable this feature, enable the 'Adapt alignment' toggle. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mod_field_list.hlp

    r3614 r6142  
    3434                REG: Simple Regular Expressions (not for beginners) 
    3535 
    36                         '/Seach RegExpr/Replace String/'  or 
    37                         '/Seach RegExpr/' 
     36                        '/Search RegExpr/Replace String/'  or 
     37                        '/Search RegExpr/' 
    3838                        (see LINK{regexpr.hlp} for more details) 
    3939 
    … …  
    4545 
    4646                        Different search/replace commands can be performed 
    47                         simultanously and have to be seperated by ':' 
     47                        simultaneously and have to be separated by ':' 
    4848 
    4949                                      ':search1=replace1:search2=replace2:  ...  :searchn=replacen'. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mode_angle.hlp

    r2986 r6142  
    5050                The scale bar and its label can be moved by positioning the 
    5151                cursor anywhere on the bar, keeping the left mouse button 
    52                 pressed, moving the cursor to the desired position and sub- 
    53                 sequently releasing the mouse button. The label of the bar 
     52                pressed, moving the cursor to the desired position and 
     53                subsequently releasing the mouse button. The label of the bar 
    5454                can be moved independently. 
    5555 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mode_info.hlp

    r2986 r6142  
    2727                Select a species or an existing group: 
    2828 
    29                         Move the cusor to the respective node and 
    30                         press the left mouse button. The corresponding infor- 
    31                         mation is displayed within the 'SPECIES INFORMATION' 
     29                        Move the cursor to the respective node and 
     30                        press the left mouse button. The corresponding 
     31                        information is displayed within the 'SPECIES INFORMATION' 
    3232                        window. 
    3333 
    3434                Create and select a group: 
    3535 
    36                         Move the cusor to any corner or edge of the triangle 
     36                        Move the cursor to any corner or edge of the triangle 
    3737                        (radial tree) or rectangle (dendrogram) representing 
    3838                        the desired group and press the right mouse button. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mode_move.hlp

    r2986 r6142  
    3838                tree topologies with respect to maximum parsimony criteria by 
    3939                moving subtrees. The current parsimony value is shown after the 
    40                 'Current Par' pormpt and can be compared with the 'Optimum Par' 
    41                 value of the iinitial tree. 
     40                'Current Par' prompt and can be compared with the 'Optimum Par' 
     41                value of the initial tree. 
    4242 
    4343 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mode_pzoom.hlp

    r2986 r6142  
    2727                        Position the cursor to define the first corner of the 
    2828                        square to magnify. Keep the left mouse button pressed 
    29                         and move the cursor to define size and positon of the 
     29                        and move the cursor to define size and position of the 
    3030                        region to magnify. Release the button. 
    3131 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/mp_params.hlp

    r2986 r6142  
    1717                - select the minimum mismatch that unmarked species should have 
    1818                  in the combination 
    19                 - for weighting mismatches there are three possiblities: 
     19                - for weighting mismatches there are three possibilities: 
    2020 
    2121                        1. all mismatches are weighted equally 
    2222 
    2323                        2. mismatches are weighted depending on which kind of 
    24                            mismatch occured 
     24                           mismatch occurred 
    2525 
    26                         3. mismatches are weighted stronger the nearer it occures 
     26                        3. mismatches are weighted stronger the nearer it occurs 
    2727                           at the center of the probe 
    2828 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/multiprobe.hlp

    r5775 r6142  
    6464                                        with target sequences. 
    6565 
    66                 Weight mismaches 
     66                Weight mismatches 
    6767 
    6868                                        If set, minor mismatches and mismatches at 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/namesadmin.hlp

    r4358 r6142  
    3737                       e.g if you import plain sequence data. 
    3838 
    39                        Use this to get rid of all nameserver entried using ARB_xxx accession 
     39                       Use this to get rid of all nameserver entries using ARB_xxx accession 
    4040                       numbers. 
    4141 
    … …  
    5454                       where it's needed.  
    5555 
    56                        For each field you use, a seperate name server will be generated. 
     56                       For each field you use, a separate name server will be generated. 
    5757                       That means: 
    5858 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/ne_compl.hlp

    r2986 r6142  
    1818                potential higher order structure elements should be studied. 
    1919 
    20                 Select a sequence by positoning the cursor on its name and 
     20                Select a sequence by positioning the cursor on its name and 
    2121                        pressing the left mouse button. 
    2222 
    … …  
    3838 
    3939                Press <REST SEQUENCE> or <REST EDITOR> to complement or 
    40                         reverse the sequence from the curent cursor position to 
     40                        reverse the sequence from the current cursor position to 
    4141                        the (right) end of the sequence or the (right) end of 
    4242                        the last (bottom) edited sequence, respectively. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/ne_pretty.hlp

    r2986 r6142  
    1010 
    1111#************* Title of helpfile !! and start of real helpfile ******** 
    12 TITLE           Printing from Eitor 
     12TITLE           Printing from Editor 
    1313 
    1414OCCURRENCE      ARB_NT/ARB_EDIT/File/Pretty Print 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/ne_replace.hlp

    r2986 r6142  
    1717                SAI entry. 
    1818 
    19                 Select a sequence by positoning the curser on the name and 
     19                Select a sequence by positioning the cursor on the name and 
    2020                        pressing the left mouse button. Position the cursor 
    2121                        within the SAI or sequence entry. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/next_neighbours.hlp

    r5785 r6142  
    3333                  * Depending on the settings of 'Search/Add/Keep species' in the main query-window 
    3434                    the species list is either replaced, added or kept. 
    35                   * Depending on the setting of 'that match/dont match the query' either the list of 
     35                  * Depending on the setting of 'that match/don't match the query' either the list of 
    3636                    found relatives is applied or the rest of the species. 
    3737 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/next_neighbours_common.hlp

    r5485 r6142  
    4949                       The 'Quick mode' works well for many sequence types and is approx. 4 times 
    5050                       faster than the 'Complete mode'. For some sequence types it completely fails, 
    51                        e.g. if there are repetetive areas containing many 'AAAAA' 
     51                       e.g. if there are repetitive areas containing many 'AAAAA' 
    5252 
    5353                Match score: 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/nt_align_select.hlp

    r941 r6142  
    1515                predicted amino acid sequences, respectively, assigned to the 
    1616                same species can be stored in one database. 
    17                 The name of the currently acessible alignment (ali_*) is shown 
     17                The name of the currently accessible alignment (ali_*) is shown 
    1818                in the respective button (ARB_NT/3rd broad rectangular 
    1919                button in top-area) 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pa_bootstrap.hlp

    r3191 r6142  
    3232                      c                 d 
    3333 
    34                 exchange a with b ( or a with d ) and count all coloums in the alignment 
     34                exchange a with b ( or a with d ) and count all columns in the alignment 
    3535                with a greater/smaller/equal minimal number of mutations 
    3636                than the original tree. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pa_quick.hlp

    r2986 r6142  
    2525 
    2626                This tool should be used for the positioning of 'species' for 
    27                 which only partial or preliminary sequence data are availble. 
     27                which only partial or preliminary sequence data are available. 
    2828 
    2929EXAMPLES        None 
    3030 
    3131WARNINGS        The phylogenetic information conferred by the new sequence(s) is 
    32                 not used for global treee optimization. 
     32                not used for global tree optimization. 
    3333 
    3434BUGS            No bugs known 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pa_quick_sel.hlp

    r2986 r6142  
    2323 
    2424                This tool should be used for the positioning of 'species' for 
    25                 which only partial or preliminary sequence data are availble. 
     25                which only partial or preliminary sequence data are available. 
    2626 
    2727EXAMPLES        None 
    2828 
    2929WARNINGS        The phylogenetic information conferred by the new sequence is 
    30                 not used for global treee optimization. 
     30                not used for global tree optimization. 
    3131 
    3232BUGS            No bugs known 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pa_ranchlengths.hlp

    r2986 r6142  
    1414 
    1515 
    16 DESCRIPTION     Calculates branch lenghts for the current tree. Branch swapping 
    17                 is used to estimate the significance of tree topologies.                 
     16DESCRIPTION     Calculates branchlengths for the current tree. Branch swapping 
     17                is used to estimate the significance of tree topologies. 
    1818 
    1919NOTES           The branch lengths reflect the significance of edges rather than 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pars.hlp

    r3614 r6142  
    2929 
    3030                Filters for the in- or exclusion of alignment columns 
    31                 ('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be seleted. 
     31                ('ARB_NT/SAI; ARB_NT/Tree/Dist Matrix) can be selected. 
    3232 
    3333                After selecting one of the parsimony items in 'Tree/Add species to existing tree' 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/parser.hlp

    r3614 r6142  
    1414 
    1515OCCURRENCE      TREE/Species/Search:PARSE FIELD 
    16                 TREE/Proporties/NDS 
     16                TREE/Properties/NDS 
    1717 
    1818 
    … …  
    2222                                and replace it by 'replace' 
    2323 
    24         Different search/replace commands can be seperated by ':': 
     24        Different search/replace commands can be separated by ':': 
    2525 
    2626                'search1=replace1:search2=replace2: ... :searchn=replacen' 
    … …  
    3030        Search && Replace string: 
    3131 
    32                 :               seperates two commands 
    33                 =               seperates the search from the replace string 
     32                :               separates two commands 
     33                =               separates the search from the replace string 
    3434                \               Escape symbol 
    3535                \\              the '\' symbol itself 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pd_spec_param.hlp

    r2986 r6142  
    2525                Define threshold for splitting melting domains: 
    2626 
    27                         Type a value to the 'Theshold for Splitting' subwindow. 
    28                         This value is substracted from the mean of all pairing 
     27                        Type a value to the 'Threshold for Splitting' subwindow. 
     28                        This value is subtracted from the mean of all pairing 
    2929                        values of the potential probe target hybrid. If the 
    3030                        resulting value is lower than that of a particular 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pfold.hlp

    r5782 r6142  
    6464        [2] DSSP 
    6565         
    66                 The DSSP program was developped to standardize secondary structure 
     66                The DSSP program was developed to standardize secondary structure 
    6767                assignment. It assigns protein secondary structures to amino acid 
    6868                sequences from the amino acids' crystallographic atom coordinates 
    … …  
    7777NOTES 
    7878 
    79         The used method for protein secondary structure prediciton, i.e. the Chou-Faman 
     79        The used method for protein secondary structure prediction, i.e. the Chou-Faman 
    8080        algorithm, is fast which was the main reason for choosing it. Performance is 
    8181        important for a large number of sequences loaded in the editor. However, it 
    … …  
    8888WARNINGS 
    8989 
    90         !!! Protein secondary sttructure in the field 'sec_struct' is not aligned 
     90        !!! Protein secondary structure in the field 'sec_struct' is not aligned 
    9191        automatically with the sequence (yet). It has to be aligned manually !!! 
    9292 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pfold_props.hlp

    r5260 r6142  
    4747        - The left textfield contains one or more amino acid pairs. Each 
    4848          pair contains two characters (amino acids, gaps-characters, ...). 
    49           Pairs are seperated by spaces (' '). 
     49          Pairs are separated by spaces (' '). 
    5050        - The right textfield contains the match symbol used for each 
    5151          of the specified pairs. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/phyl.hlp

    r2986 r6142  
    2525 
    2626                Select minimum and maximum similarities for the individual 
    27                         columns to be included for similarty or distance matrix 
     27                        columns to be included for similarity or distance matrix 
    2828                        calculation by typing the values (50 means the most 
    2929                        frequent base at a particular position is shared by at 
    … …  
    3535                        marked sequences (species) should be taken into account: 
    3636 
    37                         Use the rigth mouse button to display the submenus 
     37                        Use the right mouse button to display the submenus 
    3838                        associated to the items below the 'markerline:' prompt 
    3939                        by pressing the respective buttons. 
    … …  
    5353                                        sequences. 
    5454 
    55                                 treat as abiguous: 
     55                                treat as ambiguous: 
    5656                                        Take the respective symbol as an 
    5757                                        unambiguous residue. 
    … …  
    6060                        distance calculations: 
    6161 
    62                         Use the rigth mouse button to display the submenus 
    63                         associated to the itemss below the 'distance matrix:' 
     62                        Use the right mouse button to display the submenus 
     63                        associated to the items below the 'distance matrix:' 
    6464                        prompt by pressing the respective buttons. 
    6565 
    … …  
    7878                        Use the right mouse button to display the 'CALCULATE' 
    7979                        menu and select 'markerline' (profile) or 'distance 
    80                         matrix' by releasing the mouse button while the curser 
     80                        matrix' by releasing the mouse button while the cursor 
    8181                        is positioned on the respective menu button. 
    8282 
    … …  
    8585                        Use the right mouse button to display the 'VIEW' 
    8686                        menu and select 'species', 'markerline' or 'distance 
    87                         matrix' by releasing the mouse button while the curser 
     87                        matrix' by releasing the mouse button while the cursor 
    8888                        is positioned on the respective menu button. The names, 
    8989                        the aligment of the marked sequences and the 
    … …  
    124124                        ascii files, use the right mouse button to display the 
    125125                        'SAVE' menu and select the corresponding menu item by 
    126                         releasing the mouse button while the curser is 
     126                        releasing the mouse button while the cursor is 
    127127                        positioned on it. 
    128128 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/phylo.hlp

    r4350 r6142  
    1111TITLE           ARB_PHYLO - Create filters by base frequency 
    1212 
    13 OCCURRENCE      ARB_NT/SAI/Create Filter/by Base Frequncy 
     13OCCURRENCE      ARB_NT/SAI/Create Filter/by Base Frequency 
    1414 
    1515DESCRIPTION     Calculate base frequencies and/or a base frequency filter. 
    … …  
    5252                              The corresponding characters are counted like regular sequence characters, 
    5353                              but never interpreted as "being the most homologous character". 
    54                               Compared with 'dont count' it will result in lower base frequencies, cause 
     54                              Compared with 'don't count' it will result in lower base frequencies, cause 
    5555                              the overall number of characters occurring per column will be higher. 
    5656 
    … …  
    8585                   - all alignment columns 
    8686                   - similarity 0 to 100 
    87                    - both gaps: 'dont count (ignore)' 
     87                   - both gaps: 'don't count (ignore)' 
    8888                   - ambiguity codes: 'treat as regular character' 
    8989                   - lowercase chars: 'treat as uppercase char' 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pos_var_pars.hlp

    r2986 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile ******** 
    11 TITLE           Column - Statistik  
     11TITLE           Column statistic  
    1212 
    1313OCCURRENCE      ARB_NT/SAI/Create SAI from Sequences/Positional Variability ... 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/primer.hlp

    r2986 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile ******** 
    11 TITLE           Primer Design @@@@@@@ 
     11TITLE           Primer Design 
     12 
     13                @@@ sorry - need translation into english  
    1214 
    1315 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/probedesign.hlp

    r4935 r6142  
    9494 
    9595                Consequently, useful target sites may be not detected. 
    96                 Similarily, marked species not related to the target species and 
     96                Similarly marked species not related to the target species and 
    9797                not contained in the displayed tree will be treated as targets. 
    9898 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/probedesignresult.hlp

    r2986 r6142  
    2424                        columns of the display area, respectively. 
    2525 
    26                 The length of the psoposed probe is given in column 2. 
     26                The length of the proposed probe is given in column 2. 
    2727 
    2828                Columns 3 and 4 indicate the 5'-positions of the target sites 
    … …  
    4141                        lowered. 
    4242 
    43                         !!! The columns do only represent virtual temparature 
    44                             shifts and cannot be assigned to centigrades.!!! 
     43                        !!! The columns do only represent virtual temperature 
     44                            shifts and cannot be assigned to degree centigrade!!! 
    4545 
    4646                To write the results to an ascii file press the 'SAVE' button 
    … …  
    5151SECTION         SORTING 
    5252 
    53                 The programm brings the best probes to the front of the list. 
     53                The program brings the best probes to the front of the list. 
    5454                Best means the product 
    5555 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/probematch.hlp

    r3614 r6142  
    8686 
    8787NOTES           Unlike the 'ARB_PROBE_DESIGN' tool, the 'ARB_PROBE_MATCH' tool 
    88                 does not depend on the consistancy of the current and the 
     88                does not depend on the consistency of the current and the 
    8989                'PT_SERVER' database. Any 'PT_SERVER' database containing 
    9090                homologous or non-homologous, aligned or crude data can be 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/prompt/format_alignments.hlp

    r1626 r6142  
    1313OCCURRENCE      ARB_NT 
    1414 
    15 DESCRIPTION     Many functions of ARB expect all sequences of an alignent to 
     15DESCRIPTION     Many functions of ARB expect all sequences of an alignment to 
    1616                be of the same length (Note: "length" doesn't mean "number 
    1717                of bases" here). 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/proteinViewer.hlp

    r4186 r6142  
    1313OCCURRENCE      ARB_EDIT->View->ProteinViewer 
    1414 
    15 DESCRIPTION  Use this function to display AminoAcid sequence along with the DNA sequence. 
     15DESCRIPTION     Use this function to display AminoAcid sequence along with the DNA sequence. 
    1616                     
    17     There are six possible reading frames in every sequence, three starting at positions 1, 2 and 3 and going in 5'---->3' direction of a given sequence, and another three starting at positions 1, 2, and 3 and going in 5'--->3' direction of a given sequence of the complementary sequence. 
     17                There are six possible reading frames in every sequence, three starting at 
     18                positions 1, 2 and 3 and going in 5'---->3' direction of a given sequence, 
     19                and another three starting at positions 1, 2, and 3 and going in 5'--->3' 
     20                direction of a given sequence of the complementary sequence. 
    1821 
    19     CODON TABLE:       
    20     Select the desired codon table from the list of standard codon tables normally used in translating protein genes. 
     22                CODON TABLE: 
    2123 
    22     START POSITION:    
    23     Select the start position where the translation should begin at (base position). eg., 1, 2 or 3.  
     24                      Select the desired codon table from the list of standard codon 
     25                      tables normally used in translating protein genes. 
    2426 
    25     STRAND TYPE: 
    26     Check the "Forward Strand" to use the given sequence (as displayed) for translation. And checking "Complementary Strand" uses complementary sequence of the displayed sequence for tranlation. 
     27                START POSITION: 
    2728 
    28     By checking "Translate from database fields" , ProteinViewer extracts "translation/codon table" and "start position" from the database and uses the same for tranlation. 
     29                      Select the start position where the translation should begin at 
     30                      (base position). eg., 1, 2 or 3. 
    2931 
    30     By default, the translated (aminoacid) sequence will be displayed as single letter codes. eg., A for Arginine, etc., But you can disply three letter aminoacid code (eg., Met for methionine) in the translated sequence by checking "Display Aminoacid names" checkbox. 
     32                STRAND TYPE: 
    3133 
    32     Display options "text" and "box" will display aminoacid codes or colored boxes in the tranlated sequence, respectively. 
     34                      Check the "Forward Strand" to use the given sequence (as displayed) 
     35                      for translation. And checking "Complementary Strand" uses 
     36                      complementary sequence of the displayed sequence for translation. 
    3337 
    34     Diplay at "Marked", "Selected", "Cursor" and "All" will toggle the display of aminoacid sequence only for marked, selected, cursor position and all species in the editor, respectively. 
     38                By checking "Translate from database fields" , ProteinViewer extracts 
     39                "translation/codon table" and "start position" from the database and uses 
     40                the same for translation. 
    3541 
    36     SAVE AMINOACID SEQUENCE ALIGNMENT: 
    37     Once the alignement is refiened according to the aminoacid sequence, you can save the translated (aminoacid) sequence to the database as a new alignment. 
     42                By default, the translated (aminoacid) sequence will be displayed as 
     43                single letter codes. eg., A for Arginine, etc., But you can disply three 
     44                letter aminoacid code (eg., Met for methionine) in the translated sequence 
     45                by checking "Display Aminoacid names" checkbox. 
     46 
     47                Display options "text" and "box" will display aminoacid codes or colored 
     48                boxes in the translated sequence, respectively. 
     49 
     50                Display at "Marked", "Selected", "Cursor" and "All" will toggle the display 
     51                of aminoacid sequence only for marked, selected, cursor position and all 
     52                species in the editor, respectively. 
     53 
     54                SAVE AMINOACID SEQUENCE ALIGNMENT: 
     55 
     56                      Once the alignment is refined according to the aminoacid sequence, 
     57                      you can save the translated (aminoacid) sequence to the database as 
     58                      a new alignment. 
    3859 
    3960NOTES           None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/pt_server.hlp

    r4934 r6142  
    3333                SEARCH_PATTERNS_IN_A_BIG_DATABASE_PROGRAM. 
    3434 
    35                 We named this programm PT_SERVER ('Prefix tree server' or 
     35                We named this program PT_SERVER ('Prefix tree server' or 
    3636                synonymously 'Positional tree server'). 
    3737                The PT_SERVER searches for patterns in special database files 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rdp_ift.hlp

    r2986 r6142  
    1414 
    1515DESCRIPTION     This is a well designed reader for files from RDP. 
    16                 It reads a lot of additional informations. 
     16                It reads a lot of additional information. 
    1717 
    1818NOTES           Destination fields are tagged by [RDP]   

  • branches/stable_5.0/HELP_SOURCE/oldhelp/regexpr.hlp

    r5788 r6142  
    6969                               (e.g. '/bacter|spiri/i' matches all strings containing "bacter" or "spiri") 
    7070 
    71                   '()'         marks a subexpression. Subexpressions can be used to seperate alternatives 
     71                  '()'         marks a subexpression. Subexpressions can be used to separate alternatives 
    7272                               or to mark parts for use in the replace expression (see below). 
    7373 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rename.hlp

    r4170 r6142  
    1414 
    1515OCCURRENCE      ARB_NT/Species/Generate new names 
    16                 ARB_INTRO <MERGE TWO ARB DATABASES> ARB_MERGE <Check Consistency 
    17                 of Names> CHECK NAMES <RENAME DATASBASE .> 
     16                ARB_MERGE/Check Names/Rename species 
    1817 
    1918DESCRIPTION     Starts the 'NAME SERVER' to update names within the specified 
    20                 database according to the information storted in the file 
     19                database according to the information stored in the file 
    2120                '$ARBHOME/lib/nas/names.dat'. 
    2221 
    … …  
    2423 
    2524NOTES           It is possible to link names.dat to a central names.dat, but you should 
    26                 be aware, that there may occur temporary inconsitencies, if multiple users 
     25                be aware, that there may occur temporary inconsistencies, if multiple users 
    2726                use the nameserver at the same time. 
    2827 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rna3d_dispBases.hlp

    r4186 r6142  
    1414OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D 
    1515 
    16 DESCRIPTION     
    17     To achieve more performance and dynamic overlay of any sequence associated information, rendering (drawing) was simplified to chain display with the capacity to display residues in the form nucleotides - Adenosine (A), Guanine (G), Cytosine (C) and Uracil (U) at the respective coordinates in the molecule. Also viewing the entire chemical structure in the molecule’s 3D structure is less readable.  
     16DESCRIPTION 
     17 
     18    To achieve more performance and dynamic overlay of any sequence associated 
     19    information, rendering (drawing) was simplified to chain display with the capacity to 
     20    display residues in the form nucleotides - Adenosine (A), Guanine (G), Cytosine (C) 
     21    and Uracil (U) at the respective coordinates in the molecule. Also viewing the entire 
     22    chemical structure in the molecule’s 3D structure is less readable. 
    1823 
    1924    Display Bases 
    20     By enabling the check box the corresponding residues in the rRNA sequence can be displayed on the rRNA 3D structure. Disabling this check box will display the molecule skeleton without residues. 
     25 
     26            By enabling the check box the corresponding residues in the rRNA sequence can 
     27            be displayed on the rRNA 3D structure. Disabling this check box will display 
     28            the molecule skeleton without residues. 
    2129 
    2230    Helix Region 
    23     Enabling this check box will display residues that are participating in Helix formation in the secondary structure models of small subunit rRNA.  
     31 
     32            Enabling this check box will display residues that are participating in Helix 
     33            formation in the secondary structure models of small subunit rRNA. 
    2434 
    2535    Unpaired Helix Region 
    26     Enabling this check box will display residues that are participating in bulge (unpaired helix) formation in the secondary structure models of small subunit rRNA.  
     36 
     37            Enabling this check box will display residues that are participating in bulge 
     38            (unpaired helix) formation in the secondary structure models of small subunit 
     39            rRNA. 
    2740 
    2841    Non-Helix Region 
    29     Enabling this check box will display residues that are participating in loop (non-helix) formation in the secondary structure models of small subunit rRNA.  
     42 
     43            Enabling this check box will display residues that are participating in loop 
     44            (non-helix) formation in the secondary structure models of small subunit rRNA. 
    3045 
    3146    Display Size 
    32     The size of the residues displayed can be changed by specifying the desired size in “Display size” box. 
     47 
     48            The size of the residues displayed can be changed by specifying the desired 
     49            size in “Display size” box. 
    3350 
    3451    CHARACTERS 
    35     The corresponding residues are displayed with the actual nucleotides - Adenosine (A), Guanine (G), Cytosine (C) and Uracil (U).  
     52 
     53            The corresponding residues are displayed with the actual nucleotides - 
     54            Adenosine (A), Guanine (G), Cytosine (C) and Uracil (U). 
    3655 
    3756    SHAPES 
    38     The corresponding residues are displayed with the respective shapes specified for different structural motifs.  
    3957 
    40     By setting different colors for the secondary structural motifs (loops, stems and bulges) using “Color Settings”, the respective regions can be easily recognized in the rRNA 3D structure. 
     58            The corresponding residues are displayed with the respective shapes specified 
     59            for different structural motifs. 
     60 
     61    By setting different colors for the secondary structural motifs (loops, stems and 
     62    bulges) using “Color Settings”, the respective regions can be easily recognized in 
     63    the rRNA 3D structure. 
    4164 
    4265NOTES           None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rna3d_dispHelices.hlp

    r4186 r6142  
    1010 
    1111#************* Title of helpfile !! and start of real helpfile ******** 
    12 TITLE           Mapping Secondary Structural Infomation 
     12TITLE           Mapping Secondary Structural Information 
    1313 
    1414OCCURRENCE      In ARB primary structure editor (ARB_EDIT4) -> RNA3D 
    … …  
    1616DESCRIPTION      
    1717 
    18       Secondary and tertiary structure interactions of the well established comparative structure models of rRNA which are used in SECEDIT to generate 2D structure models are fitted to the three-dimensional structure of E. coli master sequence.  
     18    Secondary and tertiary structure interactions of the well established comparative 
     19    structure models of rRNA which are used in SECEDIT to generate 2D structure models are 
     20    fitted to the three-dimensional structure of E. coli master sequence. 
    1921 
    20     DISPLAY HELICES : Enabling this check box maps the secondary structural motifs (loops, helices and bulges) onto the molecule. Secondary structural information is according to the comparative models of rRNA used in primary and secondary structure editors.  
     22    DISPLAY HELICES: 
    2123 
    22     HELIX SKELETON : Enabling will draw a skeleton of secondary structure mask.  By setting a grey or light color you can achieve transparent mask avoiding any interference with other information overlays. 
     24            Enabling this check box maps the secondary structural motifs (loops, helices 
     25            and bulges) onto the molecule. Secondary structural information is according 
     26            to the comparative models of rRNA used in primary and secondary structure 
     27            editors. 
    2328 
    24     DISPLAY MID-HELIX : This displays middle point of the helices.  
     29    HELIX SKELETON: 
    2530 
    26     DISPLAY HELIX NUMBER : Checking this box will display the corresponding helix numbers in the rRNA 3D structure. Helix numbers are according to ARB numbering scheme.  The small subunit (16S) rRNA of E.coli contains 50 helices which are numbered from 1 to 50.  
     31            Enabling will draw a skeleton of secondary structure mask.  By setting a grey 
     32            or light color you can achieve transparent mask avoiding any interference with 
     33            other information overlays. 
    2734 
    28     DISPLAY NUMBER OF HELICES : Using this you can set the number of helices you would like to be displayed in the 3D molecule. This feature is very helpful to thoroughly examine the specific helices in the structure.  
     35    DISPLAY MID-HELIX: 
    2936 
    30     HELIX SIZE : Thickness or the size of the helices can be set by specifying the desired value in this box. 
     37            This displays middle point of the helices.  
    3138 
    32     DISPLAY TERTIARY INTERACTIONS : The tertiary interactions observed in small subunit rRNA can be displayed in the three-dimensional conformations of small subunit rRNA by enabling this check box. The tertiary information data is from Gauthert et al. 
     39    DISPLAY HELIX NUMBER: 
    3340 
    34     Color settings related to helix, skeleton, mid-helix, helix number and tertiary interactions can be changed using “Color Settings” of the main RNA3D window. 
     41            Checking this box will display the corresponding helix numbers in the rRNA 3D 
     42            structure. Helix numbers are according to ARB numbering scheme.  The small 
     43            subunit (16S) rRNA of E.coli contains 50 helices which are numbered from 1 to 
     44            50. 
     45 
     46    DISPLAY NUMBER OF HELICES: 
     47 
     48            Using this you can set the number of helices you would like to be displayed in 
     49            the 3D molecule. This feature is very helpful to thoroughly examine the 
     50            specific helices in the structure. 
     51 
     52    HELIX SIZE: 
     53 
     54            Thickness or the size of the helices can be set by specifying the desired 
     55            value in this box. 
     56 
     57    DISPLAY TERTIARY INTERACTIONS: 
     58 
     59            The tertiary interactions observed in small subunit rRNA can be displayed in 
     60            the three-dimensional conformations of small subunit rRNA by enabling this 
     61            check box. The tertiary information data is from Gautheret et al. 
     62 
     63    Color settings related to helix, skeleton, mid-helix, helix number and tertiary 
     64    interactions can be changed using “Color Settings” of the main RNA3D window. 
    3565 
    3666NOTES 
    3767                 
    38     Gautheret D, Damberger SH, Gutell RR: Identification of base-triples in RNA using comparative sequence analysis. J Mol Biol 1995, 248: 27-43. 
     68    Gautheret D, Damberger SH, Gutell RR: Identification of base-triples in RNA using 
     69    comparative sequence analysis. J Mol Biol 1995, 248: 27-43. 
    3970 
    4071 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rna3d_dispMolecule.hlp

    r4186 r6142  
    1010 
    1111#************* Title of helpfile !! and start of real helpfile ******** 
    12 TITLE           General Dislpay Options 
     12TITLE           General Display Options 
    1313 
    1414OCCURRENCE      In Primary Structure Editor (ARB_EDIT4) -> RNA3D Program 
    … …  
    1919 
    2020    Display Molecule Skeleton 
    21     Enabling this will display the entire molecule skeleton in a user-defined color. By setting a grey or light color you can achieve transparent contours of the molecule displayed avoiding its interference with the mapping information.  
    2221 
    23     SIZE : The size or thickness of the skeleton can be set by specifying the desired thickness in the “size” box. By default it is set to decimal 5.  
     22            Enabling this will display the entire molecule skeleton in a user-defined 
     23            color. By setting a grey or light color you can achieve transparent contours 
     24            of the molecule displayed avoiding its interference with the mapping 
     25            information. 
    2426 
    25     COLORIZE MOLECULE SKELETON : Based on the residues participating in secondary structural motifs (loops, helices, bulges) the molecule skeleton can be colored. Color settings with respect to secondary structural motifs can be changed using the “Color Palate” of the RNA3D interface. 
     27    SIZE: 
    2628 
    27     DISPLAY BASE POSITION : Base positions corresponding to the reference sequence (Escherichia coli) can be displayed by checking this check box. The interval of positions to be displayed can be changed by specifying the desired “interval size” at the included box. Displaying the base positions helps i) to locate probe binding sites within the molecule, ii) to refine the sequence alignments according to the molecule structure, and also iii) to identify the exact position in the primary sequence, where insertions, deletions and base substitutions occur with respect to the template sequence when a different rRNA sequence is mapped onto the master structure. 
     29            The size or thickness of the skeleton can be set by specifying the desired 
     30            thickness in the “size” box. By default it is set to decimal 5. 
    2831 
    29     ROTATE MOLECULE : Enabling this check box rotates the molecule automatically. The direction and speed of the rotation can be changed by using left mouse button and mouse movement, respectively. Alternatively, molecule can also be rotated by pressing “space bar” on the keyboard. 
     32    COLORIZE MOLECULE SKELETON: 
    3033 
    31     DISPLAY CURSOR POSITION : Checking this box will enable the cursor position to be displayed in the molecule. Cursor position is directly connected to primary structure editor (ARB_EDIT4) and any movement of cursor in ARB_EDIT4 is instantly updated in the RNA3D window.  
     34            Based on the residues participating in secondary structural motifs (loops, 
     35            helices, bulges) the molecule skeleton can be colored. Color settings with 
     36            respect to secondary structural motifs can be changed using the “Color 
     37            Palate” of the RNA3D interface. 
     38 
     39    DISPLAY BASE POSITION: 
     40 
     41            Base positions corresponding to the reference sequence (Escherichia coli) can 
     42            be displayed by checking this check box. The interval of positions to be 
     43            displayed can be changed by specifying the desired “interval size” at the 
     44            included box. Displaying the base positions helps i) to locate probe binding 
     45            sites within the molecule, ii) to refine the sequence alignments according to 
     46            the molecule structure, and also iii) to identify the exact position in the 
     47            primary sequence, where insertions, deletions and base substitutions occur 
     48            with respect to the template sequence when a different rRNA sequence is mapped 
     49            onto the master structure. 
     50 
     51    ROTATE MOLECULE: 
     52 
     53            Enabling this check box rotates the molecule automatically. The direction and 
     54            speed of the rotation can be changed by using left mouse button and mouse 
     55            movement, respectively. Alternatively, molecule can also be rotated by 
     56            pressing “space bar” on the keyboard. 
     57 
     58    DISPLAY CURSOR POSITION: 
     59 
     60            Checking this box will enable the cursor position to be displayed in the 
     61            molecule. Cursor position is directly connected to primary structure editor 
     62            (ARB_EDIT4) and any movement of cursor in ARB_EDIT4 is instantly updated in 
     63            the RNA3D window. 
    3264            
    3365 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rna3d_general.hlp

    r5711 r6142  
    1717 
    1818 
    19 OCCURRENCE      In Primary Sequnce Editor (ARB_EDIT4) 
     19OCCURRENCE      In Primary Sequence Editor (ARB_EDIT4) 
    2020 
    2121DESCRIPTION   
    2222 
    23     This program (RNA3D) displays the three-dimensional structure of small subunit (16S) rRNA in OpenGL 3D environment. The annotation of RNA three-dimensional structures consists of a preprocessing of the information embedded in their 3D coordinates. It processes PDB structural information stored in the PDB file (1M5G) and used for further structural analysis and searches. To provide user with the more detatiled perspective of 16S rRNA structure, structural information corresponding to the ribosmal protiens were excluded during processing. The extracted structural informaion is then fed to OpenGL engine, where it is further transformed into a hierarchy of OpenGL objects, which encode molecule chains, residues and base positions. At this stage, further processing may occur, for example when the user requests the mapping of secondary structure information of rRNA onto the molecule in the form of loops and stems. Any information derived from the multiple alignments (phylogenetic information) is merged into the structural information or rRNA molecule in the post-processing step.      
     23    This program (RNA3D) displays the three-dimensional structure of small subunit (16S) 
     24    rRNA in OpenGL 3D environment. The annotation of RNA three-dimensional structures 
     25    consists of a preprocessing of the information embedded in their 3D coordinates. It 
     26    processes PDB structural information stored in the PDB file (1M5G) and used for 
     27    further structural analysis and searches. To provide user with the more detailed 
     28    perspective of 16S rRNA structure, structural information corresponding to the 
     29    ribosomal proteins were excluded during processing. The extracted structural information 
     30    is then fed to OpenGL engine, where it is further transformed into a hierarchy of 
     31    OpenGL objects, which encode molecule chains, residues and base positions. At this 
     32    stage, further processing may occur, for example when the user requests the mapping of 
     33    secondary structure information of rRNA onto the molecule in the form of loops and 
     34    stems. Any information derived from the multiple alignments (phylogenetic information) 
     35    is merged into the structural information or rRNA molecule in the post-processing 
     36    step. 
    2437     
    25 NOTES            
    26     More information regarding merging secondary structure infomation and mapping individual rRNA sequence,sequence associated data, oligonucleotide probes can be found in the respective help files. See "Subtopics" section. 
     38NOTES 
     39 
     40    More information regarding merging secondary structure information and mapping 
     41    individual rRNA sequence,sequence associated data, oligo-nucleotide probes can be found 
     42    in the respective help files. See "Subtopics" section. 
    2743 
    2844EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/rna3d_mapSeqData.hlp

    r4186 r6142  
    1717 
    1818    SUPERIMPOSING rRNA SEQUENCE DATA 
    19     Any rRNA sequence contained in the multiple sequence alignments of ARB primary structure editor can be overlaid onto the structure of E. coli in the RNA3D window. Desired rRNA sequence to be mapped onto the structure can be selected by the left mouse button in the multiple sequence alignment and the selected rRNA sequence will be instantly mapped onto the master structure.  
    2019 
    21     The selected rRNA sequence is annotated with mutation (base substitutions), insertion and deletion information at each site as compared to the master sequence (E. coli).  
     20         Any rRNA sequence contained in the multiple sequence alignments of ARB primary 
     21         structure editor can be overlaid onto the structure of E. coli in the RNA3D 
     22         window. Desired rRNA sequence to be mapped onto the structure can be selected by 
     23         the left mouse button in the multiple sequence alignment and the selected rRNA 
     24         sequence will be instantly mapped onto the master structure. 
    2225 
    23     For the regions where the sequences are aligned without deletion or insertion, direct base substitution (mutation) is applied. Because the C’---C’ distance is essentially the same (~10.2 à
    24 ) in all Watson-Crick base pairs (Watson and Crick, 1953), this simple procedure preserves the base pairing and the double helical structure while substituting the bases. Although there do exist the requirement of structural adjustments for non-Watson-Crick base pairs, currently, simple base substitutions are kept because the development of new models to achieve the necessary structural adjustments is out of the scope of the RNA3D tool.  
     26         The selected rRNA sequence is annotated with mutation (base substitutions), 
     27         insertion and deletion information at each site as compared to the master 
     28         sequence (E. coli). 
    2529 
    26     In the regions where the alignment (of selected rRNA sequence) involves insertions, the respective insertion points to corresponding E. coli base position in the alignment are shown as down arrows in the crystal structure. The number of insertions and the participating nucleotides can also be displayed at the insertion points.  
     30         For the regions where the sequences are aligned without deletion or insertion, 
     31         direct base substitution (mutation) is applied. Because the C’---C’ distance 
     32         is essentially the same (~10.2 à
     33) in all Watson-Crick base pairs (Watson and 
     34         Crick, 1953), this simple procedure preserves the base pairing and the double 
     35         helical structure while substituting the bases. Although there do exist the 
     36         requirement of structural adjustments for non-Watson-Crick base pairs, currently, 
     37         simple base substitutions are kept because the development of new models to 
     38         achieve the necessary structural adjustments is out of the scope of the RNA3D 
     39         tool. 
    2740 
    28     In the case of regions, where deletions are observed in the alignment corresponding to the master sequence (E. coli), respective sites in the crystal structure are indicated as deleted. 
     41         In the regions where the alignment (of selected rRNA sequence) involves 
     42         insertions, the respective insertion points to corresponding E. coli base 
     43         position in the alignment are shown as down arrows in the crystal structure. The 
     44         number of insertions and the participating nucleotides can also be displayed at 
     45         the insertion points. 
     46 
     47         In the case of regions, where deletions are observed in the alignment 
     48         corresponding to the master sequence (E. coli), respective sites in the crystal 
     49         structure are indicated as deleted. 
    2950 
    3051    DISPLAY OPTIONS 
    3152     
    32     ENABLE MAPPING : Checking this box will enable the mapping or overlaying of any information onto the molecule globally. It is very useful to swiftly switching off mapping information. 
     53         ENABLE MAPPING: 
    3354 
    34     MAP SELECTED SPECIES :  This check box will enable mapping rRNA sequence data contained in the multiple alignments onto the 3D molecule. 
     55                Checking this box will enable the mapping or overlaying of any information 
     56                onto the molecule globally. It is very useful to swiftly switching off 
     57                mapping information. 
     58 
     59         MAP SELECTED SPECIES: 
     60 
     61                This check box will enable mapping rRNA sequence data contained in the 
     62                multiple alignments onto the 3D molecule. 
    3563  
    36     DISPLAY BASE DIFFERENCE : Enabling this check box will display the substitutions or mutations observed with respect to E.coli sequence onto 16S rRNA 3D structure.   
     64         DISPLAY BASE DIFFERENCE: 
    3765 
    38     DISPLAY BASE POSITION : Base positions corresponding to the observed substitutions or mutations in the mapped rRNA sequence are displayed by enabling this check box. 
     66                Enabling this check box will display the substitutions or mutations 
     67                observed with respect to E.coli sequence onto 16S rRNA 3D structure. 
    3968 
    40     DISPLAY DELETIONS : Enabling this check box will display deletions in mapped rRNA sequence with respect to E.coli reference sequence data.  
     69         DISPLAY BASE POSITION: 
    4170 
    42     DISPLAY INSERTIONS : Enabling this check box will display insertions in mapped rRNA sequence with respect to E.coli reference sequence data. By checking 'Bases' box, the number of insertions along with the actual bases or residues is displayed at the insertion points.  
     71                Base positions corresponding to the observed substitutions or mutations in 
     72                the mapped rRNA sequence are displayed by enabling this check box. 
    4373 
    44     DISPLAY MISSING BASES : Bases or residues which are presumed to be missing in the rRNA sequence alignments when comparing with the consensus model and/or during manual curation, can be visualized in the 3D structure. Missing bases denoted as dots ('.') in the multiple sequence alignments are mapped onto the rRNA 3D structure as question marks ('?') by enabling this check box. Such missing bases are more often attributed to errors during sequencing.  
     74         DISPLAY DELETIONS: 
    4575 
    46     Color settings related to mapped sequence data including insertions, deletions, mutations, and missing residues can be changed using 'Color Settings' of the main RNA3D window. 
     76                Enabling this check box will display deletions in mapped rRNA sequence 
     77                with respect to E.coli reference sequence data. 
    4778 
    48     MAPPING OLIGONUCLEOTIDE PROBES 
    49     The localization of the proposed oligonucleotide probe targets can be visualized in customizable background colors with in the rRNA crystal structure. Using the navigation capabilities of RNA3D tool (see “Navigation” section), one can get an idea about the probable binding site of the proposed probe with respect to the structural conformation of rRNA. 
     79         DISPLAY INSERTIONS: 
    5080 
    51     Oligonucleotide probes are designed using integrated Probe Design and Probe Match tools of ARB. The selected oligonucleotide probe in probe match window is directly mapped onto the rRNA 3D structure by enabling “Map Search Patterns” check box. 
     81                Enabling this check box will display insertions in mapped rRNA sequence 
     82                with respect to E.coli reference sequence data. By checking 'Bases' box, 
     83                the number of insertions along with the actual bases or residues is 
     84                displayed at the insertion points. 
    5285 
    53     OVERLAYING SEQUENCE ASSOCIATED INFORMATION (SAI) 
    54     Various column statistics like sequence consensus, base frequency, positional variability based on parsimony method and any other user defined column statistics that are performed on the sequence alignments can be readily overlaid onto the 3D structure.  
     86         DISPLAY MISSING BASES: 
    5587 
    56     Once the column statistics are performed, the user can define the color translation table for the chosen SAI in the ARB primary structure editor (see “View | Visualize SAIs” menu). Different colors (up to 10 colors) can be set to the values or characters stored in the SAI to visualize in the molecular structure. The molecule can be re-colored using new settings anytime by clicking the color palate button (using Color Settings in RNA3D window).  
     88                Bases or residues which are presumed to be missing in the rRNA sequence 
     89                alignments when comparing with the consensus model and/or during manual 
     90                curation, can be visualized in the 3D structure. Missing bases denoted as 
     91                dots ('.') in the multiple sequence alignments are mapped onto the rRNA 3D 
     92                structure as question marks ('?') by enabling this check box. Such missing 
     93                bases are more often attributed to errors during sequencing. 
     94 
     95         Color settings related to mapped sequence data including insertions, deletions, 
     96         mutations, and missing residues can be changed using 'Color Settings' of the main 
     97         RNA3D window. 
     98 
     99         MAPPING OLIGO-NUCLEOTIDE PROBES: 
     100 
     101                The localization of the proposed oligo-nucleotide probe targets can be 
     102                visualized in customizable background colors with in the rRNA crystal 
     103                structure. Using the navigation capabilities of RNA3D tool (see 
     104                “Navigation” section), one can get an idea about the probable binding 
     105                site of the proposed probe with respect to the structural conformation of 
     106                rRNA. 
     107 
     108                Oligo-nucleotide probes are designed using integrated Probe Design and 
     109                Probe Match tools of ARB. The selected oligo-nucleotide probe in probe 
     110                match window is directly mapped onto the rRNA 3D structure by enabling 
     111                “Map Search Patterns” check box. 
     112 
     113         OVERLAYING SEQUENCE ASSOCIATED INFORMATION (SAI): 
     114 
     115                Various column statistics like sequence consensus, base frequency, 
     116                positional variability based on parsimony method and any other user 
     117                defined column statistics that are performed on the sequence alignments 
     118                can be readily overlaid onto the 3D structure. 
     119 
     120                Once the column statistics are performed, the user can define the color 
     121                translation table for the chosen SAI in the ARB primary structure editor 
     122                (see “View | Visualize SAIs” menu). Different colors (up to 10 colors) 
     123                can be set to the values or characters stored in the SAI to visualize in 
     124                the molecular structure. The molecule can be re-colored using new settings 
     125                anytime by clicking the color palate button (using Color Settings in RNA3D 
     126                window). 
    57127     
    58     By enabling the “Map Sequence Associated Information” check box, the transformed data is readily overlaid onto the rRNA 3D structure. Any change in the SAIs and respective color transformations can be reapplied by clicking “refresh” button.  
     128                By enabling the “Map Sequence Associated Information” check box, the 
     129                transformed data is readily overlaid onto the rRNA 3D structure. Any 
     130                change in the SAIs and respective color transformations can be reapplied 
     131                by clicking “refresh” button. 
    59132 
    60133NOTES           None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/saiProbeHelp.hlp

    r2610 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile ******** 
    11 TITLE       Visualisation of Sequence Associated Information (SAI) of Probe Match Results. 
     11TITLE       Visualization of Sequence Associated Information (SAI) of Probe Match Results. 
    1212 
    1313OCCURRENCE       
    1414    In ARB primary Window (ARB_NT) : Probes (MENU) -> Match Probes (SUBMENU) 
    1515 
    16 DESCRIPTION      
    17     This window aides Visualization of Sequence Associated Informations (SAIs) of the Potential Probe Targets that were designed (PROBE DESIGN TOOL) and matched using PROBE MATCH TOOL.  
     16DESCRIPTION 
     17 
     18    This window aides Visualization of Sequence Associated Information (SAIs) of the 
     19    Potential Probe Targets that were designed (PROBE DESIGN TOOL) and matched using PROBE 
     20    MATCH TOOL. 
    1821 
    1922    Steps to be followed to VISUALIZE SAIs for the Potential Probe Targets: 
    2023 
    21     1. Select SAI to be visualized from the Select SAI Menu. (FILE -> SELECT SAI) 
     24          1. Select SAI to be visualized from the Select SAI Menu. (FILE -> SELECT SAI) 
    2225 
    23     2. Define Desired Colors (COLOR 0 to COLOR 9) for the respective CHARACTERS / NUMBERS in the selected SAI to paint as background of the Probe Targets list. (FILE -> DEFINE COLOR TRANSLATIONS) 
     26          2. Define Desired Colors (COLOR 0 to COLOR 9) for the respective CHARACTERS / 
     27          NUMBERS in the selected SAI to paint as background of the Probe Targets 
     28          list. (FILE -> DEFINE COLOR TRANSLATIONS) 
    2429 
    25     3. Values or Characters contained in the SAIs selected can also be displayed below each Probe Targets by selecting the DISPLAY SAI CHECK BOX in DEFINE COLOR TRANSLATION window. 
     30          3. Values or Characters contained in the SAIs selected can also be displayed 
     31          below each Probe Targets by selecting the DISPLAY SAI CHECK BOX in DEFINE COLOR 
     32          TRANSLATION window. 
    2633 
    27     4. Once the desired SAI is selected and the respective color translation is defined, the SAI is painted as the background of the probe targets in the defined color ranges with respect to SAIs.  
     34          4. Once the desired SAI is selected and the respective color translation is 
     35          defined, the SAI is painted as the background of the probe targets in the 
     36          defined color ranges with respect to SAIs. 
    2837     
    2938    One can change the COLOR RANGE by going to FILE -> SET COLORS AND FONTS menu. 
    3039 
    31 NOTES        
    32     Color Translation Defnitions defined for various SAIs can be saved by clicking SAVE button in DEFINE COLOR TRANSLATION window. (Press STORE to save the definitions and press RESTORE to restore the saved definitions). 
    33     To save the Color Translation Definitions permanently Go to ARB_NT window and save PROPERTIES under PROPERTIES MENU. 
     40NOTES 
     41 
     42    Color Translation Definitions defined for various SAIs can be saved by clicking SAVE 
     43    button in DEFINE COLOR TRANSLATION window. (Press STORE to save the definitions and 
     44    press RESTORE to restore the saved definitions). 
     45 
     46    To save the Color Translation Definitions permanently Go to ARB_NT window and save 
     47    PROPERTIES under PROPERTIES MENU. 
    3448 
    3549EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/saveas.hlp

    r2986 r6142  
    2323                        type the full path and file name to the subwindow 
    2424                        'FILE NAME:', press the <SAVE> button and wait until the 
    25                         'SAVE ARB DB' window disappeares. 
     25                        'SAVE ARB DB' window disappears. 
    2626 
    2727NOTES           The suffix shown in the 'SUFFIX' subwindow is appended to the 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/savedef.hlp

    r2986 r6142  
    3333SECTION GENERAL NOTES ABOUT PROPERTIES 
    3434 
    35     Mosts settings you can change in ARB are saved either 
     35    Most settings you can change in ARB are saved either 
    3636 
    3737          - to properties or 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/search_duplicates.hlp

    r5795 r6142  
    2525                perform some action on duplicates. 
    2626 
    27 NOTES           If you select 'that dont match the query' in the search window, 
     27NOTES           If you select 'that don't match the query' in the search window, 
    2828                this function instead searches for unique entries! 
    2929 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/search_equal_fields.hlp

    r6120 r6142  
    3030                Search is performed only in the field selected in the first query of DB II. 
    3131 
    32                 If you select 'that dont match' in the search&query windows, species are only listed 
     32                If you select 'that don't match' in the search&query windows, species are only listed 
    3333                if they have an entry which doesn't exist in other DB.   
    3434 
    … …  
    3838                If you need to search for empty fields, 
    3939                   * either use the second query or 
    40                    * search for '*' and select 'dont match' 
     40                   * search for '*' and select 'don't match' 
    4141 
    4242EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/searching.hlp

    r5865 r6142  
    5151                        'pyrococcus*'   matches all fields starting with 'pyrococcus' 
    5252                        '*bact*ther*'   matches all fields with the substring 'bact' followed by 'ther' 
    53                                         (there may be many characters inbetween or none, i.e. it as 
     53                                        (there may be many characters in-between or none, i.e. it as 
    5454                                        well matches 'bactther') 
    5555 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/sec_mode.hlp

    r4815 r6142  
    2828                        Right mouse button removes the clicked helix region. 
    2929 
    30                         Tipp: If you display SAI: HELIX it's easy to detect the helix 
     30                        Hint: If you display SAI: HELIX it's easy to detect the helix 
    3131                              regions. 
    3232 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/sel_fil.hlp

    r2986 r6142  
    3030 
    3131                All bases may be simplified, leaving only transversions 
    32                 and simplidfied amino-acid-groups, allowing transversion 
     32                and simplified amino-acid-groups, allowing transversion 
    3333                parsimony/fdnaml/distmethods 
    3434 
    … …  
    6464                                subwindow. 
    6565 
    66                         3. Type non-nucleotide and ambiguoity symbols to the 
     66                        3. Type non-nucleotide and ambiguity symbols to the 
    6767                                'Exclude Column' subwindow (.-acguRYS ....). 
    6868 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/sel_spec.hlp

    r2986 r6142  
    1818OCCURRENCE      ARB_NT/Species/Search 
    1919 
    20 DESCRIPTION     An Individual species can be selecetd from 'Hit list'. 
     20DESCRIPTION     An Individual species can be selected from 'Hit list'. 
    2121                The 'SPECIES INFO' window showing all 'DATABASE FIELDS' and 
    2222                the corresponding entries is initiated or updated. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/seq_quality.hlp

    r2366 r6142  
    3131                In the section "weights" you have quite a few options to fill in. 
    3232 
    33                 These are some of the criteria used to evaluate the quality of the sequences. 
     33                These are some of the criteria used to evaluate the quality of the sequences.. 
    3434                The values represent the share of the criteria in the final evaluation-formula. 
    35                 A higher value means emphasation. 
    3635                All values represent percentages, therefore all values together should sum up to 100. 
    3736 
    … …  
    6059                        of all groups of which the species is a member. 
    6160 
    62                         That comparation uses conformity with and deviation from the consensus sequence. 
     61                        That comparison uses conformity with and deviation from the consensus sequence. 
    6362 
    6463#                       A consensus is computed from sequences in one group and then from subgroups to groups. 
    6564#                        So "multilevel" consensi are generated. 
    66 #                        The value consists of two analyses: Every sequence is tested against every level of the consensus. 
     65#                        The value consists of two analysis: Every sequence is tested against every level of the consensus. 
    6766#                        Conformity and deviation from the consensus are measured. 
    6867 
    … …  
    8180                Be aware that the computation is very complex and can easily take hours to finish. 
    8281                So if you don't see the statusbar moving in the first ten minutes it just means 
    83                 that you are analysing a huge database. 
     82                that you are analyzing a huge database. 
    8483 
    8584EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/sequence_colors.hlp

    r3201 r6142  
    2727                      - In the first row you may choose which set is used for translation. 
    2828 
    29                       - The first coloumn shows the characters which should be 
     29                      - The first column shows the characters which should be 
    3030                        translated/replaced. 
    3131 
    32                       - The nth + 1 coloumn holds the data for translation set n. 
     32                      - The nth + 1 column holds the data for translation set n. 
    3333                        Each of its fields has two characters: 
    3434 
    … …  
    5858                - A simplified version of your amino acid alignment. 
    5959                - Only YR instead of ACGTU 
    60                 - Only ambigous symbols 
     60                - Only ambiguous symbols 
    6161                - ... 
    6262 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/sp_search.hlp

    r5865 r6142  
    2323 
    2424DESCRIPTION     Searches for a (set of) species (not SAIs) 
    25                 that match (dont match) a query or are marked. 
     25                that match (don't match) a query or are marked. 
    2626 
    2727                The database is scanned for 'species' (see 'HELP') 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/spaf_delete.hlp

    r2986 r6142  
    2020                display the 'DELETE FIELD' window. Select a field from the 
    2121                'Fields' subwindow and press the HIDE FIELD> 
    22                 (the field and its entry are no loger displayed in the 'SPECIES/GENE 
     22                (the field and its entry are no longer displayed in the 'SPECIES/GENE 
    2323                INFORMATION' window) or the <DELETE FIELD> (field 
    2424                and its entry are deleted) button. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/species_join.hlp

    r1171 r6142  
    2525              candidates for joining (for e.g., full_name). 
    2626 
    27             - Check seperators for fields and sequences. 
     27            - Check separators for fields and sequences. 
    2828 
    2929            - Press GO to start. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/st_ml.hlp

    r2986 r6142  
    3333 
    3434WARNINGS        This is only a prototype, don't expect something perfect. 
    35                 All sequences which should be analysed should be marked and 
     35                All sequences which should be analyzed should be marked and 
    3636                in the tree shown by ARB_NT !!!!! 
    3737 
    3838BUGS            The colors are not set correctly by default. 
    39                 The programm can only be started once. 
     39                The program can only be started once. 
    4040 
    4141SECTION         DETAILED COLUMN STATISTIC 
    … …  
    6464                displayed in color 'Range 0'. 
    6565 
    66                 [significance is 90% (hardcoded) - will be made utilisable soon] 
     66                [significance is 90% (hardcoded) - will be made utilizable soon] 
    6767 
    6868                The single (or two) base character(s) responsive for the 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/tbl_scale.hlp

    r2764 r6142  
    1919                (i.e. when the treeing program has an error) in which case ARB has 
    2020                assumed that branchlengths are in range [0 .. 100] and 
    21                 has devided them by 100. 
     21                has divided them by 100. 
    2222 
    2323EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/tkeep_mrkd.hlp

    r2986 r6142  
    2222WARNINGS        !!! No 'undo' function available yet !!! 
    2323 
    24                 It is rekommended to copy the tree before modifying it. 
     24                It is recommended to copy the tree before modifying it. 
    2525 
    2626BUGS            no bugs 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/tr_type_irs.hlp

    r2986 r6142  
    2424 
    2525DESCRIPTION     Trees can be displayed as dendrograms or radial trees. 
    26                 Dendograms have two styles: The normal style and the 
    27                 IRS style. 
     26 
     27                Dendrograms have two styles: 
     28                    * The normal style and 
     29                    * the IRS style. 
     30 
    2831                To display the IRS style dendrogram press the third small button 
    2932                below the tree_name in the top area. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/trans_anal.hlp

    r2986 r6142  
    1010 
    1111#************* Title of helpfile !! and start of real helpfile ******** 
    12 TITLE           Transversion Analyses 
     12TITLE           Transversion analysis 
    1313 
    1414OCCURRENCE      in all filter windows 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/translate_dna_2_pro.hlp

    r5600 r6142  
    4343 
    4444                2. Select reading frame by pressing the 'Start position' button 
    45                    and selecting first, second or third absolut position. 
     45                   and selecting first, second or third absolute position. 
    4646                   Alternatively you can position the cursor in ARB_EDIT4 at start 
    4747                   of the reading frame. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/tree2file.hlp

    r2986 r6142  
    4949                                        Total Tree = Full tree 
    5050 
    51                 Select a file name from the 'Directories and Files' subwindow 
    52                         or type it to the 'File Name' subwindow. 
     51                Select a file name from the 'Directories and Files' subwindow or type it 
     52                to the 'File Name' subwindow. 
    5353 
    5454                Save and/or edit the data: 
    … …  
    5757                        'Export TREE TO FILE' window 
    5858 
    59                                 - SAVE:         exports the data 
     59                                - SAVE: 
    6060 
    61                                 - S & XFIG      Writes the data to the speci- 
    62                                                 fied file and edits the file. 
    63                                                 (xfig language has to selected) 
     61                                    exports the data 
    6462 
    65                                 - S & GHOST     Writes the data to the speci- 
    66                                                 fied file and displays the 
    67                                                 preview. (postscript language 
    68                                                 has to be selected). The 
    69                                                 previewer allows tree printing. 
     63                                - S & XFIG 
     64 
     65                                    Writes the data to the specified file and edits the file. 
     66                                    (xfig language has to selected) 
     67 
     68                                - S & GHOST 
     69 
     70                                    Writes the data to the specified file and displays the 
     71                                    preview. (postscript language has to be selected). The 
     72                                    previewer allows tree printing. 
    7073 
    7174 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/trm_del.hlp

    r2986 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile ******** 
    11 TITLE           Remove Zoombies 
     11TITLE           Remove Zombies 
    1212 
    13 OCCURRENCE      ARB_NT/Tree/Remove Zoombies 
     13OCCURRENCE      ARB_NT/Tree/Remove Zombies 
    1414 
    1515DESCRIPTION     Removes 'deleted' species from the currently displayed tree. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/undo.hlp

    r2986 r6142  
    2222                - changing the cursor position in ARB_EDIT4 does not affect DB 
    2323                - changing dialogs does _sometimes_ affect DB (this depends 
    24                   on whether the value is temporary or permanent). 
     24                  on whether the value is save in properties or in the DB). 
    2525 
    2626                Note that there is only _one_ undo/redo queue for all applications 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/version.hlp

    r3614 r6142  
    1919        1.0:    1993-94         Openwin Version 
    2020 
    21         2.0.0b  Juni 95         Full Motif Version, 
     21        2.0.0b  June 95         Full Motif Version, 
    2222                                Phylip included, 
    2323                                Final database but untested 
    … …  
    2828                                save/load branch labels to NEWICK Format 
    2929 
    30         2.1.0   Nov             GDE editor can save 
     30        2.1.0   November        GDE editor can save 
    3131                                NEW ALI editor from Niels, Fogt ... 
    3232                                a lot of bug fixes: 
    … …  
    3434                                        - recover from corrupt database 
    3535                                        ... 
    36         2.1.1   Jan             GDE is working now 
    37                                 compress matrixes is possible 
     36        2.1.1   January 96      GDE is working now 
     37                                compressing matrices is possible 
    3838 
    39                 April           Vacation 
    40  
    41                 Mai             Save Changes as 
     39                May             Save Changes as 
    4240                                Parsimony inserts species sorted by sequence length 
    4341                                bug fixes:      - import by readseq improved 
    … …  
    5856                                bug fix: probes for groups 
    5957 
    60         2.4b    Oktober         Tags implemented, Tags can be used to subdivide fields 
     58        2.4b    October         Tags implemented, Tags can be used to subdivide fields 
    6159                                resize of most windows does work 
    6260 
    … …  
    6866                December        Linux Version 
    6967 
    70                 Januar          Macros 
     68                January 97      Macros 
    7169 
    7270                February        One major bug fixed in the database system 
    … …  
    7977                                Merge preserves alignment 
    8078 
    81                 Feb'99          ARB_EDIT4 now is the default editor. 
     79                February 99     ARB_EDIT4 now is the default editor. 
    8280                                Code for amino-DNA-translation/realignment 
    8381                                completely rewritten. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/visualizeSAI.hlp

    r1660 r6142  
    99 
    1010#************* Title of helpfile !! and start of real helpfile ******** 
    11 TITLE           Visualisation of Sequence Associated Information (SAI) in Primary and Secondary Editors. 
     11TITLE           Visualization of Sequence Associated Information (SAI) in Primary and Secondary Editors. 
    1212 
    1313OCCURRENCE      In Sequence Editors - Primary Editor (ARB_EDIT4) and Secondary Editor 
    1414 
    15 DESCRIPTION This function can be used to Visualise Sequence Associated Informations (SAI) in the Primary Structure and Secondary Structure Editor windows. 
     15DESCRIPTION 
     16 
     17            This function can be used to Visualize Sequence Associated Information (SAI) 
     18            in the Primary Structure and Secondary Structure Editor windows. 
    1619             
    17             Steps to use VISUALISATION of SAIs in Primary Structure Editor: 
     20            Steps to use VISUALIZATION of SAIs in Primary Structure Editor: 
    1821 
    19                1. Select SAI to be visualised from the SAI list (all SAIs present in the ARB Database).   
    20                2. Select the Color Translation Table (CTT) in the CTT list, if found. Or create one by pressing CREATE button. You can also copy the existing CTT and modify. 
    21                3. Once CTT is created, define desired colors (RANGE 0 to RANGE 9) for the respective characters in the selected SAI to paint as background of the sequence. 
    22                4. You can also change the COLOR RANGE by going to PROPERTIES->CHANGE COLORS AND FONTS menu. 
    23                5. Then, choose the visualisation options. You can opt to visualise only MARKED species or ALL species in the primary editor. 
    24                6. Finally, be sure to check ENABLE VISUALISATION check box. 
     22               1. Select SAI to be visualized from the SAI list (all SAIs present in the 
     23               ARB Database). 
    2524 
    26             If Color Translation Tables were defined for each existing/displayed SAIs in the Primary Editor, one can navigate through different SAIs in the editor and visulaize the same instantly. To enable this feature, AUTOSELECT SAI should be enabled in Visualize SAI window (VIEW->VISUALIZE SAIs menu). 
     25               2. Select the Color Translation Table (CTT) in the CTT list, if found. Or 
     26               create one by pressing CREATE button. You can also copy the existing CTT 
     27               and modify. 
    2728 
    28             Sequence Associated Information can also be visualised in Secondary Structure Editor.         
     29               3. Once CTT is created, define desired colors (RANGE 0 to RANGE 9) for the 
     30               respective characters in the selected SAI to paint as background of the 
     31               sequence. 
     32 
     33               4. You can also change the COLOR RANGE by going to PROPERTIES->CHANGE 
     34               COLORS AND FONTS menu. 
     35 
     36               5. Then, choose the visualization options. You can opt to visualize only 
     37               MARKED species or ALL species in the primary editor. 
     38 
     39               6. Finally, be sure to check ENABLE VISUALIZATION check box. 
     40 
     41            If Color Translation Tables were defined for each existing/displayed SAIs in 
     42            the Primary Editor, one can navigate through different SAIs in the editor and 
     43            visualize the same instantly. To enable this feature, AUTOSELECT SAI should be 
     44            enabled in Visualize SAI window (VIEW->VISUALIZE SAIs menu). 
     45 
     46            Sequence Associated Information can also be visualized in Secondary Structure 
     47            Editor. 
    2948     
    30                To Visualise SAI in Secondary Structure editor window - Go to PROPERTIES menu, click on CHANGE DISPLAY sub-menu and select Visulaise SAI check box. 
     49               To Visualize SAI in Secondary Structure editor window - Go to PROPERTIES 
     50               menu, click on CHANGE DISPLAY sub-menu and select the 'Visualize SAI' check 
     51               box. 
    3152 
    32                You can also change the colors used to display SAIs by going to PROPERTIES->CHANGE COLORS AND FONTS menu in the Secondary Editor Window. 
     53               You can also change the colors used to display SAIs by going to 
     54               PROPERTIES->CHANGE COLORS AND FONTS menu in the Secondary Editor Window. 
    3355 
    34 NOTES       If SAIs are to be visualised in Secondary Structure Editor window, one should select SAI, define CTT and check ENABLE VISUALISATION check box in Primary structure editor window using VISUALISE SAI function (under VIEW menu in PRIMARY EDITOR). 
     56NOTES       If SAIs are to be visualized in Secondary Structure Editor window, one should 
     57            select SAI, define CTT and check ENABLE VISUALIZATION check box in Primary 
     58            structure editor window using VISUALIZE SAI function (under VIEW menu in 
     59            PRIMARY EDITOR). 
    3560             
    36             Inorder to retain the settings of CTT and associated SAIs, one should save the properties by going to PROPERTIES->SAVE PROPERTIES menu in primary editor. Plese note that the CTT definitions are stored in the local file (.arb_prop/edit4.arb) and deleting or modifying this file will lose all the information about CTT definitions used for visualization of SAIs for future sessions.  
     61            In order to retain the settings of CTT and associated SAIs, one should save 
     62            the properties by going to PROPERTIES->SAVE PROPERTIES menu in primary 
     63            editor. Please note that the CTT definitions are stored in the local file 
     64            (.arb_prop/edit4.arb) and deleting or modifying this file will lose all the 
     65            information about CTT definitions used for visualization of SAIs for future 
     66            sessions. 
    3767 
    3868EXAMPLES        None 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/vn_search.hlp

    r1444 r6142  
    1515 
    1616DESCRIPTION     Allow the user to select a appropriate valid name from the list 
    17                 of available names manually. This is neccessary because the automatic suggestion works 
     17                of available names manually. This is necessary because the automatic suggestion works 
    1818                only for 100% identical entries. A preselection from the list of all 
    1919                available names can be made by giving any number of initial characters. 
    2020                A name selection in the list can then assigned to the current selected species 
    21                 and is written to the fiels Valid_Names/NameString, description type then is manually. 
     21                and is written to the fields Valid_Names/NameString, description type then is manually. 
    2222 
    2323 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/vn_suggest.hlp

    r1444 r6142  
    1515 
    1616DESCRIPTION     Looks in the list of valid names for perfect matching entry with a species full name. 
    17                 Either a valid name, a heronym, a homonym or change of name. 
     17                Either a valid name, a heteronym, a homonym or change of name. 
    1818                On matching the the valid name is written to a new database container 
    1919                called Valid_Name in the field NameString. A second field of this container called DescType 
    2020                tells about the species full name's status. I.e. whether it is the valid name, a heteronym, 
    21                 a homonym or mispelled. Three letters indicate species or genus, and three letter the status. 
     21                a homonym or misspelled. Three letters indicate species or genus, and three letter the status. 
    2222 
    2323NOTES           Subspecies are not taken into account yet. 

  • branches/stable_5.0/HELP_SOURCE/oldhelp/write_field_list.hlp

    r2986 r6142  
    4141 
    4242 
    43 WARNINGS        Exept for the 'name' field, there are no different protection 
     43WARNINGS        Except for the 'name' field, there are no different protection 
    4444                levels for different fields. Take care not to write to  fields 
    4545                which should contain unique entries for the corresponding 

  • branches/stable_5.0/Makefile

    r6122 r6142  
    2626# The ARB source code is aware of the following defines: 
    2727# 
    28 # NDEBUG                doesnt compile the DEBUG sections 
     28# NDEBUG                doesn't compile the DEBUG sections 
    2929# DEVEL_$(DEVELOPER)    developer-dependent flag (enables you to have private sections in code) 
    3030#                       DEVELOPER='ANY' (default setting) will be ignored 
    … …  
    193193 
    194194cflags += -pipe 
    195 cflags += -fmessage-length=0# dont wrap compiler output 
     195cflags += -fmessage-length=0# don't wrap compiler output 
    196196cflags += -funit-at-a-time 
    197197cflags += -fPIC 
    … …  
    242242 
    243243GL_LIBS:=# no opengl -> no libs 
    244 GL:=# dont build ARB openGL libs 
     244GL:=# don't build ARB openGL libs 
    245245 
    246246endif 
    … …  
    366366                @echo ' modified     - rebuild files modified in svn checkout (touches files!)' 
    367367                @echo '' 
    368                 @echo 'Internal maintainance:' 
     368                @echo 'Internal maintenance:' 
    369369                @echo '' 
    370370                @echo ' release     - build a release (increases minor version number)' 
    … …  
    939939 
    940940#*************************************************************************************** 
    941 #                       Recursive calls to submakefiles 
     941#                       Recursive calls to sub-makefiles 
    942942#*************************************************************************************** 
    943943 

  • branches/stable_5.0/PERL2ARB/DOC.html

    r2273 r6142  
    5353                        ... 
    5454                ARB:commit_transaction($gb_main);       // everything is ok 
    55                 $error = ARB::save($gb_main,"new_db.arb", "a"); // save in ascii frmt 
     55                $error = ARB::save($gb_main,"new_db.arb", "a"); // save in ascii format 
    5656 
    5757        ***************************** END 1 ********************* 
    … …  
    253253                a               ascii format 
    254254                b               binary format 
    255         Only if you have opened a database on a file your are allowd to 
     255        Only if you have opened a database on a file you are allowed to 
    256256        save it, otherwise the server has to do it. 
    257257        You may not change the path of the database, it is used 
    … …  
    267267 
    268268$error = ARB::save_quick_as($gb_main,"new path"); 
    269         Fake an existing database by create a symbolik link and 
     269        Fake an existing database by create a symbolic link and 
    270270        then call ARB::save_quick 
    271271 
    … …  
    287287        Increments an internal counter. If the counter was previously 
    288288        0 then calls begin_transaction. This is usefull when working 
    289         in a soubroutine and not knowing whether your calling funtion 
     289        in a subroutine and not knowing whether your calling function 
    290290        had opened a transaction already. 
    291291$error = ARB::pop_transaction($gb_main); 
    … …  
    313313        search a database element if all keys are unique 
    314314 
    315 $gb_xxx = ARB::find($gb_start_sourch_point, "[key]", "[value]", 
     315$gb_xxx = ARB::find($gb_start_search_point, "[key]", "[value]", 
    316316        "search_mode" 
    317317 
    … …  
    344344$val = ARB::read_bits($gb_xxx,char_0,char_1); 
    345345        convert a bit array into a string, 
    346         a '0' will be convertet into char_0 
     346        a '0' will be converted into char_0 
    347347        a '1' into char_1 
    348348 
    … …  
    362362                                // char_0 will converted to 1 else 0 
    363363 
    364 $error = ARB::write_as_string($gb_xxx); try to interprete the value and 
     364$error = ARB::write_as_string($gb_xxx); try to interpret the value and 
    365365                                // convert it automatically to the right 
    366366                                // format 
    … …  
    422422$error = ARB::set_temporary($gb_xxx); 
    423423        Marks a field in the database as a temporary field. 
    424         That means that this fiels is never saved to a file. 
     424        That means that this field is never saved to a file. 
    425425$error = ARB::clear_temporary($gb_xxx); 
    426426        Clears tmp flag 
    … …  
    502502$time = ARB::last_saved_clock($gb_main); 
    503503        transaction number when the database was last saved 
    504         Can only be called from the server programm 
     504        Can only be called from the server program 
    505505 
    506506$time = ARB::last_saved_time($gb_main); 
    … …  
    509509$error = ARB::set_cache_size($gb_main, "size_in_bytes"); 
    510510        ARB uses datacompression for long strings. If some strings 
    511         are used very intensivly the program bay slow down. 
     511        are used very intensely the program may slow down. 
    512512        Therefor a small cache is used and it's size can be set 
    513513        by this function. If you are working with sequences, a value 

  • branches/stable_5.0/arb_CHANGES.txt

    r6111 r6142  
    2626 - Distance matrix (arb_dist): mark by distance to selected 
    2727 - ARB core 
    28    * many bugfixes and improvements to reliabilty 
     28   * many bugfixes and improvements to reliability 
    2929   * faster sorting (general speedup) 
    3030   * improved sequence compression (avoid worse trees, better ratio) 
    … …  
    6969 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives 
    7070   several new possibilities: 
    71    * export taxonony via 'Export NDS list' 
     71   * export taxonomy via 'Export NDS list' 
    7272   * display taxonomy in Editor etc. 
    7373   * display of cascaded taxonomies 
    … …  
    140140 - Binary SAIs are editable in ARB_EDIT4 
    141141 - Information windows are detachable (allows to have multiple windows showing different items) 
    142  - Scanning for hidden/unknown database fields improved and seperated; 
     142 - Scanning for hidden/unknown database fields improved and separated; 
    143143   possibility to remove unused fields. 
    144144 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.) 

  • branches/stable_5.0/arb_INSTALL.txt

    r6059 r6142  
    1616 
    1717  * the detailed list of packets to install for ARB:    arb_UBUNTU.txt 
    18   * the package-install-skript for ubuntu:              SH/arb_installubuntu4arb.sh 
     18  * the package-install-script for ubuntu:              SH/arb_installubuntu4arb.sh 
    1919 
    2020-------------------------------------------------------------------------------- 

  • branches/stable_5.0/arb_LICENSE.txt

    r5431 r6142  
    180180 
    181181        convert_aln --  an alignment(or sequence) converter written by Wen-Min Kuan 
    182                         for the Ribsomal Database Project(RDP), April 28, 1992. 
    183  
    184  
    185  
    186     TREETOOL 
    187  
    188         Written by Mike Maciukenas, at the RDP, with design and 
    189         implementation guidance by Gary Olsen, Niels Larsen, Carl 
    190         Woese. 
    191  
    192         Copyright (c) 1991, University of Illinois board of 
    193         trustess. All rights reserved. 
    194  
    195         Treetool is a copyrighted program, not in the public 
    196         domain. It is provided free of charge, and permission is 
    197         granted to copy and dirstribute, provided that it is not done 
    198         for profit, and that all copyright messages remain present and 
    199         intact. 
     182                        for the Ribosomal Database Project(RDP), April 28, 1992. 
    200183 
    201184 

  • branches/stable_5.0/arb_README.txt

    r6042 r6142  
    6161        Change your .cshrc/.profile files: 
    6262 
    63                 Set the enviroment variable ARBHOME 
     63                Set the environment variable ARBHOME 
    6464                to the ARB installation directory 
    6565                Append   $ARBHOME/bin   to your PATH 

  • branches/stable_5.0/arb_UBUNTU.txt

    r6097 r6142  
    5858 
    5959[Note:] 
    60 You may use the provided install skript, e.g. 
     60You may use the provided install script, e.g. 
    6161    sudo SH/arb_installubuntu4arb.sh 

  • branches/stable_5.0/doc/a2ps.README

    r5390 r6142  
    11This is version 4.3 of a2ps, a program to format an ascii file for 
    2 printing in a postcript printer. As the copyright indicates, this 
     2printing on a postscript printer. As the copyright indicates, this 
    33distribution can be freely redistributed. 
    44 
    … …  
    2727       use in general 11.0 x 8.5. 
    2828    b) Total lateral (left+right) or vertical (top+bottom) margins. It must 
    29        be also a real constant, specifying inchs (by default 1.2). 
     29       be also a real constant, specifying inches (by default 1.2). 
    3030       - MARGIN 
    3131    c) Directory separator (by default '/') 

  • branches/stable_5.0/etc/files

    r5390 r6142  
    22DIRECTORIES 
    33 
    4                 bin             binaries: arb_programms and links to DEPOT 
     4                bin             binaries: arb programs and external tools 
    55 
    66                SH              /bin/sh commands 
    77 
    8                 DEPOT           external programms (phylip blast ..) 
    9                 DEPOT/xfig      xfig 
    10                 DEPOT/ghostview 
    11                 DEPOT/phylip 
    12                 DEPOT/etc 
    13                 DEPOT/gde 
    14  
    158                GDEHELP         GDE help Files and menus 
    169 
    17                 man             manuals, but not for man 
    18                 Xlib            X11 libraries 
    19  
    20                 lib             All libraries 
    21                 lib/pts         The pt_server files 
     10                lib             Shared libraries 
     11                lib/pts         The PT_server files 
    2212                lib/nas         The name server files 
    23                 lib/pictures    All xfig background graphics 
     13                lib/pictures    All xfig window layouts 
    2414                lib/pixmaps     All pixmaps 
    25                 lib/arb_prop    Default defaults 
     15                lib/arb_prop    Default properties 
    2616                lib/submit      submission forms 
    27                 lib/help        all arb help files               
     17                lib/help        ARB help files 
     18                lib/help_html   HTML version of ARB help 
    2819 
    2920 

  • branches/stable_5.0/lib/pictures/RNA3D_Help.fig

    r3948 r6142  
    1991996 990 6885 7020 7110 
    2002004 2 -1 0 0 18 12 0.0000 4 165 450 7020 7065 $help\001 
    201 4 0 -1 0 0 2 14 0.0000 4 165 5400 990 7020 For detailed help regarding respective diplay buttons click \001 
     2014 0 -1 0 0 2 14 0.0000 4 165 5400 990 7020 For detailed help regarding respective display buttons click \001 
    202202-6 
    2032032 1 0 1 0 7 50 0 -1 0.000 0 0 -1 0 0 1 
    … …  
    2202204 0 -1 0 0 0 13 0.0000 4 165 4410 2925 4365 : Redraws the structure with new settings/changes\001 
    2212214 0 -1 0 0 0 13 0.0000 4 165 3960 2925 4005 : Removes the cut / Displays entire molecule\001 
    222 4 0 -1 0 0 0 13 0.0000 4 150 4320 2925 3645 : Cuts the molecule at the centre for clear view\001 
     2224 0 -1 0 0 0 13 0.0000 4 150 4320 2925 3645 : Cuts the molecule at the center for clear view\001 
    2232234 0 -1 0 0 0 13 0.0000 4 165 3600 2925 3285 : DISABLEs the respective display option\001 
    2242244 0 -1 0 0 0 13 0.0000 4 165 3510 2925 2925 : ENABLEs the respective display option\001 

  • branches/stable_5.0/lib/pictures/ad_ext.fig

    r1670 r6142  
    32324 2 -1 0 0 18 13 0.0000 4 195 990 6600 2925 $to:X:copy\001 
    33334 0 -1 0 0 18 12 0.0000 4 165 915 4800 3375 $X:remark\001 
    34 4 1 -1 0 0 18 15 0.0000 4 225 3660 3750 1125 Sequence Associated Informations\001 
     344 1 -1 0 0 18 15 0.0000 4 225 3660 3750 1125 Sequence Associated Information\001 
    35354 2 -1 0 0 18 13 0.0000 4 180 825 4575 4800 $to:X:list\001 

  • branches/stable_5.0/lib/pictures/arb_intro.fig

    r6014 r6142  
    35354 0 -1 0 0 18 12 0.0000 4 195 840 9150 10440 $Y:expert\001 
    36364 0 -1 0 0 18 12 0.0000 4 180 420 1500 5865 $box\001 
    37 4 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Direcories (D)\001 
     374 0 -1 0 0 18 12 0.0000 4 195 2970 1500 5340 Existing Files (f) and Directories (D)\001 
    38384 0 -1 0 0 18 12 0.0000 4 180 540 1620 10395 $Y:old\001 
    39394 0 -1 0 0 18 12 0.0000 4 180 540 4725 10388 $Y:del\001 

  • branches/stable_5.0/lib/pictures/awt/col_statistic.fig

    r2 r6142  
    554 0 18 12 0 -1 0 0.00000 4 15 38 99 69 $close 
    664 2 18 12 0 -1 0 0.00000 4 15 31 499 69 $help 
    7 4 1 18 12 0 -1 0 0.00000 4 15 188 299 79 Use COLOUMN STATISTIC (CSP) 
     74 1 18 12 0 -1 0 0.00000 4 15 188 299 79 Use COLUMN STATISTIC (CSP) 
    884 1 18 12 0 -1 0 0.00000 4 15 252 299 97 to estimate G+C, rates, TT-ratio and weights 
    994 0 18 12 0 -1 0 0.00000 4 15 28 89 159 $box 
    … …  
    13134 0 18 12 0 -1 0 0.00000 4 15 185 99 134 Select a CSP from the database: 
    14144 0 18 12 0 -1 0 0.00000 4 15 34 94 519 $helix 
    15 4 0 18 12 0 -1 0 0.00000 4 15 359 94 314 coloumn. This results in a great variance, which can be avoided 
     154 0 18 12 0 -1 0 0.00000 4 15 359 94 314 column. This results in a great variance, which can be avoided 
    16164 0 18 12 0 -1 0 0.00000 4 15 205 94 334 by smoothing the parameter values. 

  • branches/stable_5.0/lib/pictures/awt/parser.fig

    r2 r6142  
    21214 1 18 12 0 -1 0 0.00000 4 15 101 179 122 contents of fields. 
    22224 1 18 12 0 -1 0 0.00000 4 15 50 179 140 You can: 
    23 4 1 18 12 0 -1 0 0.00000 4 15 125 179 158 * subsitute substrings 
     234 1 18 12 0 -1 0 0.00000 4 15 125 179 158 * substitute substrings 
    24244 1 18 12 0 -1 0 0.00000 4 15 145 179 176 *copy one field to another 
    25254 1 18 12 0 -1 0 0.00000 4 15 124 179 212 sequence information 

  • branches/stable_5.0/lib/pictures/consensus/max_freq.fig

    r570 r6142  
    44         319 399 319 39 79 39 79 399 319 399 9999 9999 
    554 2 18 12 0 -1 0 0.00000 4 15 31 314 64 $help 
    6 4 1 18 12 0 -1 0 0.00000 4 15 157 199 89 For each coloumn calculate 
     64 1 18 12 0 -1 0 0.00000 4 15 157 199 89 For each column calculate 
    774 1 18 12 0 -1 0 0.00000 4 15 197 199 107 the frequency of the most frequent 
    884 1 18 12 0 -1 0 0.00000 4 15 59 199 125 character. 

  • branches/stable_5.0/lib/pictures/conservProfile2Gnuplot.fig

    r1463 r6142  
    10106 1710 5445 6030 6705 
    11114 0 -1 0 0 2 10 0.0000 4 105 840 5175 5580 MAXIMUM\001 
    12 4 0 -1 0 0 2 10 0.0000 4 105 975 3330 5580 MINIMUMM\001 
     124 0 -1 0 0 2 10 0.0000 4 105 975 3330 5580 MINIMUM\001 
    13134 0 -1 0 0 18 12 0.0000 4 165 600 4950 6075 $maxX\001 
    14144 0 -1 0 0 18 12 0.0000 4 165 600 4950 6660 $maxY\001 

  • branches/stable_5.0/lib/pictures/cpro/csp_2_gnuplot.fig

    r569 r6142  
    1515         9045 11790 
    16164 0 -1 0 0 18 12 0.0000 4 165 570 1350 975 $close\001 
    17 4 0 -1 0 0 18 12 0.0000 4 180 2625 1425 1425 Select your coloumn statistic\001 
     174 0 -1 0 0 18 12 0.0000 4 180 2625 1425 1425 Select your column statistic\001 
    18184 0 -1 0 0 18 12 0.0000 4 180 420 1350 1800 $csp\001 
    19194 1 -1 0 0 18 12 0.0000 4 165 540 4200 9000 $save\001 

  • branches/stable_5.0/lib/pictures/di_ge_ma.fig

    r5416 r6142  
    59594 0 -1 0 0 18 12 0.0000 4 135 570 6000 5400 enable\001 
    60604 0 -1 0 0 18 12 0.0000 4 135 1395 1275 4800 Exclude Column\001 
    61 4 0 -1 0 0 18 12 0.0000 4 180 1845 1275 4200 Weigths/Rates/GC ...\001 
     614 0 -1 0 0 18 12 0.0000 4 180 1845 1275 4200 Weights/Rates/GC ...\001 
    62624 0 -1 0 0 18 12 0.0000 4 135 450 1275 3600 Filter\001 
    63634 0 -1 0 0 18 12 0.0000 4 165 1065 3975 6750 $autodetect\001 

  • branches/stable_5.0/lib/pictures/edit4/search.fig

    r4384 r6142  
    28286 5700 6975 9075 7650 
    29294 0 -1 0 0 0 10 0.0000 4 165 3060 5700 7200 Use '?' as single letter wildcard \001 
    30 4 0 -1 0 0 0 10 0.0000 4 165 4950 5700 7425 Use ',' or newline as seperator between search patterns\001 
     304 0 -1 0 0 0 10 0.0000 4 165 4950 5700 7425 Use ',' or newline as separator between search patterns\001 
    31314 0 -1 0 0 0 10 0.0000 4 165 3960 5700 7650 '#' initiates a comment for a search pattern\001 
    3232-6 

  • branches/stable_5.0/lib/pictures/gde2item.fig

    r2 r6142  
    19194 0 18 13 0 -1 0 0.00000 4 15 37 79 264 Filter: 
    20204 0 18 13 0 -1 0 0.00000 4 15 70 129 269 $filtername 
    21 4 0 18 12 0 -1 0 0.00000 4 15 94 49 224 COLOMNFILTER 
     214 0 18 12 0 -1 0 0.00000 4 15 94 49 224 COLUMNFILTER 
    22224 0 18 12 0 -1 0 0.00000 4 15 77 49 339 PARAMETER 
    23234 0 18 13 0 -1 0 0.00000 4 15 89 404 229 $compression 

  • branches/stable_5.0/lib/pictures/gde3item.fig

    r4041 r6142  
    11114 0 18 13 0 -1 0 0.00000 4 15 37 79 239 Filter: 
    12124 0 18 13 0 -1 0 0.00000 4 15 70 129 244 $filtername 
    13 4 0 18 12 0 -1 0 0.00000 4 15 94 49 199 COLOMNFILTER 
     134 0 18 12 0 -1 0 0.00000 4 15 94 49 199 COLUMNFILTER 
    1414-6 
    15156 294 189 494 239 

  • branches/stable_5.0/lib/pictures/join_species.fig

    r1155 r6142  
    17174 1 -1 0 0 18 14 0.0000 4 210 6135 4800 2025 joins all marked species which have the same value in field:\001 
    18184 0 -1 0 0 18 12 0.0000 4 135 525 1575 2625 FIELD\001 
    19 4 0 -1 0 0 18 12 0.0000 4 180 2865 4770 3015 Seperate database entries with:\001 
     194 0 -1 0 0 18 12 0.0000 4 180 2865 4770 3015 Separate database entries with:\001 
    20204 0 -1 0 0 18 12 0.0000 4 180 495 4770 3415 $sym\001 
    21214 0 -1 0 0 18 12 0.0000 4 180 735 5985 3420 $to:sym\001 
    22 4 0 -1 0 0 18 12 0.0000 4 180 2220 4770 3815 Seprate sequences with:\001 
     224 0 -1 0 0 18 12 0.0000 4 180 2220 4770 3815 Separate sequences with:\001 
    23234 0 -1 0 0 18 12 0.0000 4 180 810 4770 4215 $symseq\001 
    24244 0 -1 0 0 18 12 0.0000 4 180 1050 5985 4215 $to:symseq\001 

  • branches/stable_5.0/lib/pictures/merge/mg_mergetaggedfield.fig

    r2 r6142  
    12124 0 18 12 0 -1 0 0.00000 4 15 109 89 514 Tag Name of Field1 
    13134 0 18 12 0 -1 0 0.00000 4 15 109 369 514 Tag Name of Field2 
    14 4 0 18 12 0 -1 0 0.00000 4 15 104 109 114 Fiieldname of DB1 
     144 0 18 12 0 -1 0 0.00000 4 15 104 109 114 Fieldname of DB1 
    15154 0 18 12 0 -1 0 0.00000 4 15 101 394 114 Fieldname of DB2 
    16164 0 18 12 0 -1 0 0.00000 4 15 45 89 144 $fields1 

  • branches/stable_5.0/lib/pictures/pars/kernlin.fig

    r6089 r6142  
    94944 0 18 12 0 -1 0 0.00000 4 15 39 239 384 $static 
    95954 0 18 12 0 -1 0 0.00000 4 15 298 54 174 Number of randomly chosen nodes from the subtree 
    96 4 0 18 12 0 -1 0 0.00000 4 15 166 54 379 Enable static path  reduction: 
     964 0 18 12 0 -1 0 0.00000 4 15 166 54 379 Enable static path reduction: 
    97974 0 18 12 0 -1 0 0.00000 4 15 119 69 414 Pathes in each depth 
    98984 0 18 12 0 -1 0 0.00000 4 15 84 69 529 Relative Costs 
    … …  
    1041044 0 0 10 0 -1 0 0.00000 4 12 40 74 629 start costs 
    1051054 0 18 10 0 -1 0 0.00000 4 12 28 74 659 $start 
    106 4 0 18 10 0 -1 0 0.00000 4 12 274 69 309 Each rekursion step multiplies the number of paths by 8 
     1064 0 18 10 0 -1 0 0.00000 4 12 274 69 309 Each recursion step multiplies the number of paths by 8 
    1071074 0 18 10 0 -1 0 0.00000 4 12 337 69 324 (e.g. depth = 8  -> ~16 million paths -> two heuristic path reductions) 
    1081084 0 18 10 0 -1 0 0.00000 4 12 257 69 189 ( 0.0 == no nodes, 1.0 all nodes,  2.0 all nodes twice) 
    1091094 0 18 12 0 -1 0 0.00000 4 15 180 54 484 Enable dynamic path reduction: 
    110 4 0 0 10 0 -1 0 0.00000 4 12 101 339 533 getrs worse than this line 
    111 4 0 0 10 0 -1 0 0.00000 4 12 85 339 519 Stop rekursion if tree 
     1104 0 0 10 0 -1 0 0.00000 4 12 101 339 533 get's worse than this line 
     1114 0 0 10 0 -1 0 0.00000 4 12 85 339 519 Stop recursion if tree 
    1121124 1 18 12 0 -1 0 0.00000 4 15 271 239 119 K.L. is a heuristic  approach to find the best tree 
    1131134 0 18 12 0 -1 0 0.00000 4 15 236 54 254 If a better tree is found, increase depth by 

  • branches/stable_5.0/lib/pictures/pd_main.fig

    r2823 r6142  
    45454 0 -1 0 0 18 12 0.0000 4 135 1080 5925 4575 G+C-content\001 
    46464 0 -1 0 0 18 12 0.0000 4 180 675 765 6075 $design\001 
    47 4 1 -1 0 0 18 12 0.0000 4 180 5670 5325 1440 This module searches for specific oligonocleotids in the database. \001 
     474 1 -1 0 0 18 12 0.0000 4 180 5670 5325 1440 This module searches for specific oligo-nucleotides in the database. \001 
    48484 1 -1 0 0 18 12 0.0000 4 180 7185 5325 1710 Note: The PT_SERVER's (not the current) database is used searching probe targets!\001 
    49494 0 -1 0 0 18 12 0.0000 4 180 465 2250 1050 $help\001 

  • branches/stable_5.0/lib/pictures/seq_quality.fig

    r5391 r6142  
    2102104 2 -1 0 0 18 13 0.0000 4 210 1020 6255 4410 $to:X:tree\001 
    2112114 0 -1 0 0 18 13 0.0000 4 210 525 1080 2745 $tree\001 
    212 4 0 -1 0 0 18 13 0.0000 4 210 4875 1080 2295 Select a tree to define groups to analyse (opt.):\001 
     2124 0 -1 0 0 18 13 0.0000 4 210 4875 1080 2295 Select a tree to define groups to analyze (opt.):\001 
    2132134 1 -1 0 0 2 18 0.0000 4 255 3210 3465 1575 Calculate sequence quality\001 
    2142144 2 -1 0 0 18 12 0.0000 4 195 510 6030 1080 $help\001 

  • branches/stable_5.0/lib/pictures/unused/findcorr/bc_fa.fig

    r2 r6142  
    23232 2 0 1 -1 0 0 0 0.000 0 0 0 
    2424         569 359 569 39 139 39 139 359 569 359 9999 9999 
    25 4 0 18 13 0 -1 0 0.00000 4 15 98 159 89 Standardisation 
     254 0 18 13 0 -1 0 0.00000 4 15 98 159 89 Standardization 
    26264 2 18 13 0 -1 0 0.00000 4 15 74 549 94 $ztrafo_orig 
    27274 0 18 13 0 -1 0 0.00000 4 15 172 159 219 z-Transformation of factors 

  • branches/stable_5.0/lib/pictures/unused/findcorr/bc_fat.fig

    r2 r6142  
    22224 0 18 13 0 -1 0 0.00000 4 15 77 79 239 Maximum of 
    23234 0 18 13 0 -1 0 0.00000 4 15 134 79 259 summed Eigenvalues 
    24 4 0 18 13 0 -1 0 0.00000 4 15 92 79 299 communalities 
     244 0 18 13 0 -1 0 0.00000 4 15 92 79 299 commonalities 
    25254 0 18 13 0 -1 0 0.00000 4 15 79 79 159 Minimum of  
    26264 0 18 13 0 -1 0 0.00000 4 15 137 79 279 Minimum of summed  

  • branches/stable_5.0/lib/pictures/unused/findcorr/bc_verb.fig

    r2 r6142  
    15154 0 18 13 0 -1 0 0.00000 4 17 107 99 239 (parameter room) 
    16164 0 18 13 0 -1 0 0.00000 4 17 73 99 264 data matrix  
    17 4 0 18 13 0 -1 0 0.00000 4 17 103 99 224 covarince matrix 
     174 0 18 13 0 -1 0 0.00000 4 17 103 99 224 covariance matrix 
    18184 0 18 13 0 -1 0 0.00000 4 17 74 99 304 covariances 
    19194 0 18 13 0 -1 0 0.00000 4 17 148 99 344 transformation matrices 
    … …  
    25254 0 18 13 0 -1 0 0.00000 4 15 40 59 429 $close 
    26264 1 18 13 0 -1 0 0.00000 4 15 31 239 89 $info 
    27 4 0 18 13 0 -1 0 0.00000 4 17 179 79 184 addtional commented output 
     274 0 18 13 0 -1 0 0.00000 4 17 179 79 184 additional commented output 
    28284 0 18 13 0 -1 0 0.00000 4 17 56 319 144 $verbose 
    29294 0 18 13 0 -1 0 0.00000 4 17 115 79 139 additional verbose 

  • branches/stable_5.0/lib/pictures/unused/findcorr/bc_verb2.fig

    r2 r6142  
    15154 0 18 13 0 -1 0 0.00000 4 15 40 59 269 $close 
    16164 0 18 13 0 -1 0 0.00000 4 17 16 279 169 no 
    17 4 0 18 13 0 -1 0 0.00000 4 17 179 79 199 addtional commented output 
     174 0 18 13 0 -1 0 0.00000 4 17 179 79 199 additional commented output 
    18184 0 18 13 0 -1 0 0.00000 4 17 20 259 199  on 
    19194 2 18 13 0 -1 0 0.00000 4 17 65 384 229 $comment 

  • branches/stable_5.0/lib/pictures/unused/logo.fig

    r5886 r6142  
    335 1 0 40 -1 7 0 0 0.000 0 0 0 404.720 279.720 304 279 333 209 404 179 
    446 79 279 559 319 
    5 4 0 6 23 0 0 3 0.00000 4 30 477 79 319 Development of a phylogenetic enviroment 
     54 0 6 23 0 0 3 0.00000 4 30 477 79 319 Development of a phylogenetic environment 
    66-6 
    771 1 0 0 0 20 0 21 0.00000 1 0.000 459 219 120 60 459 219 579 279 

  • branches/stable_5.0/lib/pictures/visualizeSAI.fig

    r1654 r6142  
    1991994 0 -1 0 0 18 14 0.0000 4 195 975 1305 4050 $clrTrList\001 
    2002004 2 -1 0 0 18 14 0.0000 4 195 1260 5130 6165 $to:clrTrList\001 
    201 4 0 -1 0 0 2 14 0.0000 4 135 1545 1035 6705 Visualise SAI for \001 
     2014 0 -1 0 0 2 14 0.0000 4 135 1545 1035 6705 Visualize SAI for \001 
    2022024 1 -1 0 0 18 13 0.0000 4 180 795 4635 6750 $marked\001 
    203203-6 

  • branches/stable_5.0/util/arb_srclst.pl

    r6116 r6142  
    237237  my $matches = matchingExpr($str,@$regexp_arr_r); 
    238238  if ($matches>0) { 
    239     if ($debug_matching!=0) { print "'$str' matches '".$$regexp_arr_r[$matches-1]."' => dont use!\n"; } 
     239    if ($debug_matching!=0) { print "'$str' matches '".$$regexp_arr_r[$matches-1]."' => don't use!\n"; } 
    240240    $$use_r = 0; 
    241241  } 

  • branches/stable_5.0/util/arb_test_compresssion

    r2 r6142  
    3535arb_2_ascii test.$1/$1_o2m.arb test.$1/$1_o2m_a.arb 
    3636 
    37 echo '    reganerate binary ascii' 
     37echo '    regenerate binary ascii' 
    3838arb_2_bin test.$1/$1_a.arb test.$1/$1_ab.arb 
    3939arb_2_ascii test.$1/$1_ab.arb test.$1/$1_aba.arb