| 1 | ARB change log |
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| 2 | |
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| 3 | Major changes for next release: |
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| 4 | |
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| 5 | - Detect clusters of species with similar sequences (OTUs) in ARB_DIST |
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| 6 | - Rewrote chimera check. Allows filtering |
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| 7 | - added RNACMA (computes clusters of correlated positions) |
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| 8 | - Next relative search |
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| 9 | - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences) |
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| 10 | - corrected and improved scaling of relative scores |
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| 11 | - fast-aligner |
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| 12 | - searches next-relatives based on selected column-block |
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| 13 | - align multiple column-blocks based on SAI |
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| 14 | - Rewrote alignment adaption during merge |
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| 15 | - EDIT4 |
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| 16 | - improved support for using multiple edit-windows |
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| 17 | - smoother refreshes |
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| 18 | - tweaked ORF display |
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| 19 | - consense trees |
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| 20 | - calculate from multiple existing trees |
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| 21 | - fixed NJ-bootstrapping (no longer drops species) |
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| 22 | - trees sortable now |
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| 23 | - tree display |
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| 24 | - Show brackets on open groups (dendrogram tree only) |
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| 25 | - rewrote IRS (folded) display |
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| 26 | - tweaked printing (interface, overlapping) |
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| 27 | - automation |
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| 28 | - tweaked macro recording |
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| 29 | - arb_ntree can execute macro from command line |
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| 30 | - added "Never ask again" to modal question boxes (for better compatibility with macros) |
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| 31 | - load/save for window specific settings (e.g. allows to share parts of configuration with other users) |
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| 32 | - Support for mouse-wheel |
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| 33 | - many internal refactorings |
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| 34 | |
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| 35 | |
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| 36 | Fixes for arb_5.3: |
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| 37 | |
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| 38 | * bugfixes |
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| 39 | - fixed wrong absolute/ecoli position reported for some designed probes |
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| 40 | - decompression error handling (pt-server build issues) |
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| 41 | - fixed 'codon_start' generated with wrong type |
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| 42 | - fixed a buffer overflow in ACI |
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| 43 | - report failures to write to /tmp |
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| 44 | * changes |
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| 45 | - markSpecies.pl: |
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| 46 | mark by accession number |
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| 47 | partial/ambiguous matches |
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| 48 | * internal fixes |
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| 49 | - compilation fixes for OSX |
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| 50 | - some patches for debian version (removed refs to xview, textedit, removed molphy(protml)) |
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| 51 | - removed obsolete dependency from libXp |
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| 52 | |
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| 53 | |
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| 54 | Fixes for arb_5.2: |
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| 55 | |
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| 56 | * bugfixes |
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| 57 | - quicksave did silently do nothing (especially not save anything) if an error occurred |
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| 58 | - ARB_EDIT4: crashed when using config with MANY unknown species |
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| 59 | - ARB_SECEDIT: crashed when trying to paint strand w/o any base |
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| 60 | - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo |
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| 61 | * changes |
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| 62 | - ARB uses xdg-open to display web-pages |
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| 63 | * internal fixes |
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| 64 | - karmic koala (gcc 4.4.1) |
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| 65 | - installation script |
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| 66 | - arb build process uses xsltproc instead of sablotron |
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| 67 | |
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| 68 | |
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| 69 | Fixes for arb_5.1: |
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| 70 | |
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| 71 | * fixed a bug in 'Create species from consensus' (created sequence was corrupted) |
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| 72 | * fixed 2 bugs in optimize DB (alignment w/o data, missing transaction) |
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| 73 | * updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell) |
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| 74 | * fixed broken demo.arb |
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| 75 | |
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| 76 | |
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| 77 | Major changes for arb_5.00: |
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| 78 | |
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| 79 | - ARB 64bit version |
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| 80 | - new genome importer |
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| 81 | - search for next relatives improved (normal search and fast-aligner) |
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| 82 | * new parameters to precise search |
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| 83 | * improved speed |
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| 84 | * partial sequence reach normal scores |
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| 85 | - search&query |
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| 86 | * supports regular expressions and ACI |
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| 87 | * track hit information |
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| 88 | * result sorting |
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| 89 | - Nameservers with add.field have to be started with default value |
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| 90 | You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat) |
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| 91 | - multiple PT-servers may be used in parallel |
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| 92 | - fixed multiprobe |
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| 93 | - type-conversion for DB fields |
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| 94 | - SILVA compatible import filters |
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| 95 | - Newick tree export: |
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| 96 | * optionally save in human-readable format (big) |
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| 97 | * closer to newick standard format (quoting style, comment, special chars in data) |
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| 98 | - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface) |
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| 99 | - Fixed sequence quality calculation |
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| 100 | - Secondary structures for proteins (DSSP) |
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| 101 | - Distance matrix (arb_dist): mark by distance to selected |
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| 102 | - ARB core |
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| 103 | * many bugfixes and improvements to reliability |
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| 104 | * faster sorting (general speedup) |
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| 105 | * improved sequence compression (avoid worse trees, better ratio) |
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| 106 | * improved handling of temporary files (permission/removal) |
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| 107 | * prints backtraces in userland |
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| 108 | * regular expression are POSIX standard now |
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| 109 | - macro record/playback |
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| 110 | * fixed several bugs |
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| 111 | * you need to re-record your old macros! |
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| 112 | - GUI: |
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| 113 | * disabled auto-focus, you need to click now |
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| 114 | * auto-raise windows on access |
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| 115 | - Minor things: |
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| 116 | * Ubuntu: packet installation for ARB |
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| 117 | * Fixed novice/expert mode |
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| 118 | * Mark deep/degenerated branches |
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| 119 | * Increased NDS entries |
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| 120 | - up-to-date Mac port (thx to Matt Cottrell) |
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| 121 | |
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| 122 | Major changes in ARB 07.12.07org: |
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| 123 | |
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| 124 | - rewrote secondary structure editor |
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| 125 | - Sequence quality check |
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| 126 | - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc) |
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| 127 | - tweaked base frequency filter generation |
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| 128 | - Normal export (not using readseq) improved: |
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| 129 | * supports filters and gap removal |
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| 130 | * optimized for big amount of data |
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| 131 | * reworked export filters |
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| 132 | - Display translation with different ORFs in EDIT4 |
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| 133 | - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse. |
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| 134 | - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool) |
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| 135 | - more compact display in EDIT4 |
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| 136 | - capable to use iso10646 fonts |
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| 137 | - supports various gcc versions (2.95.3 - 4.1.1) |
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| 138 | - fixed a bug in DB optimization (occurred when fields had bigger protection than current) |
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| 139 | - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses |
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| 140 | different color for size-limited circles; fixed xfig-export-bug |
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| 141 | - Allows Branchlength <-> Bootstrap value transfer (lossy!) |
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| 142 | - fixed several scaling bugs in "folded tree"-mode |
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| 143 | - improved import-filter error-messages |
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| 144 | - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives |
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| 145 | several new possibilities: |
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| 146 | * export taxonomy via 'Export NDS list' |
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| 147 | * display taxonomy in Editor etc. |
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| 148 | * display of cascaded taxonomies |
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| 149 | * display taxonomy of tree_1 in tree_2 |
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| 150 | * allows to write taxonomy into database field of species |
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| 151 | * compare taxonomies of two trees |
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| 152 | * ... |
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| 153 | - ACI: |
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| 154 | * many new ACI commands |
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| 155 | * unified handling of binary ACI-operators |
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| 156 | * tracing of ACI actions for debugging purpose |
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| 157 | - ARB Neighbour joining: |
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| 158 | * bootstrap limit configurable |
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| 159 | * bugfix: when aborting bootstrap calculation, sometimes no tree was generated |
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| 160 | - EDIT4: |
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| 161 | * added unalign right (block-op) |
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| 162 | * added 'Save loaded properties' |
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| 163 | - GENE MAP: |
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| 164 | * multiple views possible at the same time |
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| 165 | * origin now at "12 o'clock" |
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| 166 | * implemented 'jump to gene' |
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| 167 | - tweaked file selection |
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| 168 | - Enhanced Search Depth for Probe Match --> max 20 MM |
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| 169 | - CLUSTALW: |
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| 170 | * separated menus for fast and slow alignment |
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| 171 | * most parameters accessible from inside ARB now |
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| 172 | - upgraded to PHYLIP 3.6 (adds PROML) |
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| 173 | - external programs may be called parallel (e.g. several treeing programs) |
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| 174 | - fixed bugs in protml and integration of protml |
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| 175 | - rewrote ASCII database import |
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| 176 | - arb_repair for databases of any size (script for database repair) |
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| 177 | - fixed bug in data compression |
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| 178 | - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse) |
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| 179 | - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000) |
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| 180 | - GDE menus cleanup |
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| 181 | - translation/re-alignment tweaked |
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| 182 | - unalign right (EDIT4) |
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| 183 | - visualization of SAIs in Probe Match Results |
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| 184 | - changed formatting of probe match results; increase # of allowed matches to 100.000; |
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| 185 | warn if results are truncated |
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| 186 | - PT server for genes |
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| 187 | - Probe design performance optimized |
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| 188 | - fixed NEXUS export format |
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| 189 | - exports group names into Newick format |
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| 190 | - import XML tree files |
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| 191 | - help for external tools now properly shown inside ARB |
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| 192 | |
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| 193 | Major changes in Beta 2003_08_22: |
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| 194 | |
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| 195 | - automatic formatting of alignments |
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| 196 | - SECEDIT may use EDIT4 colors |
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| 197 | - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!)) |
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| 198 | - updated clustalw to version 1.83 |
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| 199 | - Restore window sizes for ALL windows (too small sizes are ignored) |
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| 200 | - new algorithm to add partial sequences to an existing tree |
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| 201 | - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony |
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| 202 | - Top area of ARB_NTREE may be reduced to maximize display area |
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| 203 | - All arb menus may be detached (click dashed line at top of menu) |
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| 204 | - visualization of SAIs (as background color behind Sequences) |
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| 205 | - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties |
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| 206 | - PT-server occupies more memory => does less passes; more diagnostic output |
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| 207 | - small changes to status window (unhide behavior/time estimation) |
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| 208 | - menus and menu-hotkeys reorganized |
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| 209 | - colored buttons in color config windows |
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| 210 | - alignment concatenation (e.g. several different genes) |
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| 211 | - merging data of similar species (according selected database field) |
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| 212 | - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand) |
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| 213 | - expanded sellists |
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| 214 | - save/load fixed for multi probes |
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| 215 | - Binary SAIs are editable in ARB_EDIT4 |
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| 216 | - Information windows are detachable (allows to have multiple windows showing different items) |
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| 217 | - Scanning for hidden/unknown database fields improved and separated; |
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| 218 | possibility to remove unused fields. |
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| 219 | - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.) |
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| 220 | - updated fastDNAml to 1.2.2 |
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| 221 | - added AxML (accelerated fastDNAml 1.2.2) |
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| 222 | - Field transfer definitions for exporting gene-species |
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| 223 | - File Selection: - recursive search available |
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| 224 | - The ARB_NTREE macro recording/execution has been fixed |
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| 225 | - Colorize species (see demo.arb) |
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| 226 | - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display |
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| 227 | - 'IslandHopper' -- a new integrated aligner (beta) |
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| 228 | - Many improvements and bugfixes to secondary structure editor: |
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| 229 | * highlighting of search (i.e for probes) like in EDIT4 |
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| 230 | * interactive constraint editing (stretch/compress) |
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| 231 | * probe info |
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| 232 | * editing secondary structure in XFIG now possible |
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| 233 | * visualization of SAIs |
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| 234 | - import reads Unix, DOS, and MAC linefeeds |
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| 235 | - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help |
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| 236 | - tree and sequence export to XML ( DTDs are provided in ./lib/dtd ) |
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| 237 | (reloading of these XML files is planned for the future) |
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| 238 | - fixed problems with phylip-tree import/export (bootstrap values,comments,...) |
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| 239 | - search in all database fields possible ('[all fields]') |
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| 240 | - up to 10 quicksaves are kept |
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| 241 | - new ACI functions: upper, lower, caps, eval |
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| 242 | - variables for import filter programming |
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| 243 | - extract gene-species: creates acc; extraction to existing alignments |
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| 244 | - sequence of selected gene is mirrored in ARB_EDIT4/local_signature |
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| 245 | (=> selected gene can be highlighted in primary editor) |
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| 246 | - PCR primer-design for single genes |
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| 247 | - when selecting a gene, the corresponding gene-species is selected (if found) |
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| 248 | - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...) |
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| 249 | - file selection box in import window |
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| 250 | - mark item with double click works in all search&query windows |
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| 251 | - User masks: create new; 'edit enable' and 'marked' toggles (like in info window) |
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| 252 | - Fixed command line help for all Arb-modules |
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| 253 | - Fixed problem parsing fonts (should fix display problems with default fonts) |
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| 254 | - Mark mode now works in list-view as well (ARB_NTREE) |
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| 255 | - Fixed appearance of 'tiny little boxes' (everywhere) |
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| 256 | - Redesign of ARB help: |
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| 257 | - a HTML version is in $ARBHOME/lib/help_html |
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| 258 | - a text version is in $ARBHOME/lib/help (like before, but now generated) |
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| 259 | |
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| 260 | Major changes in Beta 2001_11_07: |
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| 261 | |
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| 262 | - design probes to maximum length of 60 nucleotides |
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| 263 | - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode) |
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| 264 | - import default changed to foreign data format, ali name '16s' |
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| 265 | - printing of multi-page-trees works again |
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| 266 | - implemented user defineable masks to access database fields |
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| 267 | - fixed bugs in pt-server (lockup, unknown species just after building pt-server) |
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| 268 | - improved performance during pt-server-build |
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| 269 | - several programs coming along with ARB where updated (PHYLIP,...) |
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| 270 | - reads EMBL genom files |
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| 271 | - support for experiments (genom databases only) |
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| 272 | |
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| 273 | Major changes in Beta 2001_07_24: |
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| 274 | |
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| 275 | - basic support for genoms (Gene Map, reads Genebank files) |
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| 276 | - ported to libc6 |
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