source: tags/svn.1.5.4/arb_CHANGES.txt

ARB change log

Major changes for next release:

 - Show brackets on open groups (dendrogram tree only)
 - Detect clusters of species with similar sequences (OTUs) in ARB_DIST
 - Rewrote chimera check. Allows filtering
 - Rewrote alignment adaption during merge
 - ORF display:
   - arc does not cross characters
   - Fixed colors of amino names
 - load/save for window specific settings (e.g. allows to share parts of configuration
   with other users)
 - many internal refactorings


Fixes for arb_5.2:

 * bugfixes
   - quicksave did silently do nothing (especially not save anything) if an error occurred 
   - ARB_EDIT4: crashed when using config with MANY unknown species
   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
 * changes
   - ARB uses xdg-open to display web-pages
 * internal fixes
   - karmic koala (gcc 4.4.1)
   - installation script
   - arb build process uses xsltproc instead of sablotron 


Fixes for arb_5.1:

 * fixed a bug in 'Create species from consensus' (created sequence was corrupted)
 * fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
 * updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
 * fixed broken demo.arb


Major changes for arb_5.00:

 - ARB 64bit version
 - new genome importer
 - search for next relatives improved (normal search and fast-aligner)
   * new parameters to precise search
   * improved speed
   * partial sequence reach normal scores
 - search&query
   * supports regular expressions and ACI
   * track hit information
   * result sorting
 - Nameservers with add.field have to be started with default value
   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
 - multiple PT-servers may be used in parallel
 - fixed multiprobe
 - type-conversion for DB fields
 - SILVA compatible import filters
 - Newick tree export:
   * optionally save in human-readable format (big)
   * closer to newick standard format (quoting style, comment, special chars in data)
 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
 - Fixed sequence quality calculation
 - Secondary structures for proteins (DSSP)
 - Distance matrix (arb_dist): mark by distance to selected
 - ARB core
   * many bugfixes and improvements to reliability
   * faster sorting (general speedup)
   * improved sequence compression (avoid worse trees, better ratio)
   * improved handling of temporary files (permission/removal)
   * prints backtraces in userland
   * regular expression are POSIX standard now
 - macro record/playback
   * fixed several bugs
   * you need to re-record your old macros!
 - GUI:
   * disabled auto-focus, you need to click now
   * auto-raise windows on access
 - Minor things:
   * Ubuntu: packet installation for ARB
   * Fixed novice/expert mode
   * Mark deep/degenerated branches
   * Increased NDS entries
 - up-to-date Mac port (thx to Matt Cottrell)

Major changes in ARB 07.12.07org:

 - rewrote secondary structure editor
 - Sequence quality check
 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
 - tweaked base frequency filter generation
 - Normal export (not using readseq) improved:
   * supports filters and gap removal
   * optimized for big amount of data
   * reworked export filters
 - Display translation with different ORFs in EDIT4
 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
 - more compact display in EDIT4
 - capable to use iso10646 fonts
 - supports various gcc versions (2.95.3 - 4.1.1)
 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
   different color for size-limited circles; fixed xfig-export-bug
 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
 - fixed several scaling bugs in "folded tree"-mode
 - improved import-filter error-messages
 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
   several new possibilities:
   * export taxonomy via 'Export NDS list'
   * display taxonomy in Editor etc.
   * display of cascaded taxonomies
   * display taxonomy of tree_1 in tree_2
   * allows to write taxonomy into database field of species
   * compare taxonomies of two trees
   * ...
 - ACI:
   * many new ACI commands
   * unified handling of binary ACI-operators
   * tracing of ACI actions for debugging purpose
 - ARB Neighbour joining:
   * bootstrap limit configurable
   * bugfix: when aborting bootstrap calculation, sometimes no tree was generated
 - EDIT4:
   * added unalign right (block-op)
   * added 'Save loaded properties'
 - GENE MAP:
   * multiple views possible at the same time
   * origin now at "12 o'clock"
   * implemented 'jump to gene'
 - tweaked file selection
 - Enhanced Search Depth for Probe Match --> max 20 MM
 - CLUSTALW:
   * separated menus for fast and slow alignment
   * most parameters accessible from inside ARB now
 - upgraded to PHYLIP 3.6 (adds PROML)
 - external programs may be called parallel (e.g. several treeing programs)
 - fixed bugs in protml and integration of protml
 - rewrote ASCII database import
 - arb_repair for databases of any size (script for database repair)
 - fixed bug in data compression
 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000) 
 - GDE menus cleanup
 - translation/re-alignment tweaked
 - unalign right (EDIT4)
 - visualization of SAIs in Probe Match Results
 - changed formatting of probe match results; increase # of allowed matches to 100.000;
   warn if results are truncated
 - PT server for genes
 - Probe design performance optimized
 - fixed NEXUS export format
 - exports group names into Newick format
 - import XML tree files
 - help for external tools now properly shown inside ARB

Major changes in Beta 2003_08_22:

 - automatic formatting of alignments
 - SECEDIT may use EDIT4 colors
 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
 - updated clustalw to version 1.83
 - Restore window sizes for ALL windows (too small sizes are ignored)
 - new algorithm to add partial sequences to an existing tree
 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
 - Top area of ARB_NTREE may be reduced to maximize display area
 - All arb menus may be detached (click dashed line at top of menu)
 - visualization of SAIs (as background color behind Sequences)
 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
 - PT-server occupies more memory => does less passes; more diagnostic output
 - small changes to status window (unhide behavior/time estimation)
 - menus and menu-hotkeys reorganized
 - colored buttons in color config windows
 - alignment concatenation (e.g. several different genes)
 - merging data of similar species (according selected database field)
 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
 - expanded sellists
 - save/load fixed for multi probes
 - Binary SAIs are editable in ARB_EDIT4
 - Information windows are detachable (allows to have multiple windows showing different items)
 - Scanning for hidden/unknown database fields improved and separated;
   possibility to remove unused fields.
 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
 - updated fastDNAml to 1.2.2
 - added AxML (accelerated fastDNAml 1.2.2)
 - Field transfer definitions for exporting gene-species
 - File Selection: - recursive search available
 - The ARB_NTREE macro recording/execution has been fixed
 - Colorize species (see demo.arb)
 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
 - 'IslandHopper' -- a new integrated aligner (beta)
 - Many improvements and bugfixes to secondary structure editor:
   * highlighting of search (i.e for probes) like in EDIT4
   * interactive constraint editing (stretch/compress)
   * probe info
   * editing secondary structure in XFIG now possible
   * visualization of SAIs
 - import reads Unix, DOS, and MAC linefeeds
 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
   (reloading of these XML files is planned for the future)
 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
 - search in all database fields possible ('[all fields]')
 - up to 10 quicksaves are kept
 - new ACI functions: upper, lower, caps, eval
 - variables for import filter programming
 - extract gene-species: creates acc; extraction to existing alignments
 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
   (=> selected gene can be highlighted in primary editor)
 - PCR primer-design for single genes
 - when selecting a gene, the corresponding gene-species is selected (if found)
 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
 - file selection box in import window
 - mark item with double click works in all search&query windows
 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
 - Fixed command line help for all Arb-modules
 - Fixed problem parsing fonts (should fix display problems with default fonts)
 - Mark mode now works in list-view as well (ARB_NTREE)
 - Fixed appearance of 'tiny little boxes' (everywhere)
 - Redesign of ARB help:
     - a HTML version is in $ARBHOME/lib/help_html
     - a text version is in $ARBHOME/lib/help (like before, but now generated)

Major changes in Beta 2001_11_07:

 - design probes to maximum length of 60 nucleotides
 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
 - import default changed to foreign data format, ali name '16s'
 - printing of multi-page-trees works again
 - implemented user defineable masks to access database fields
 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
 - improved performance during pt-server-build
 - several programs coming along with ARB where updated (PHYLIP,...)
 - reads EMBL genom files
 - support for experiments (genom databases only)

Major changes in Beta 2001_07_24:

 - basic support for genoms (Gene Map, reads Genebank files)
 - ported to libc6