ARB change log

Major changes for next release:

 - ARB PARSIMONY
   * topology optimization
     - now (by default) strictly restricted to marked/visible parts of the tree (#640)
     - restriction now customizable (marked/all; visible/all)
     - tree costs for protein-data were not independent from root-position (as expected by model; #633).
       Caused infinite running optimization under some circumstances.
     - optimize-modes now strictly restrict to clicked subtrees. single/repeated optimization possible.
     - KL-optimizer
       * static path reduction slightly changed meaning. changed default settings.
       * removed randomness (was just covering some bugs)
       * improved general optimization speed
   * branchlength calculation
     - "forgot" to recalculate lengths under some conditions. fixed.
     - is now independent of tree-root position (#641)
   * adding species
     - 'add partial species' failed if two partial species had NO overlap (#609). fixed.
     - in 'add species + NNI' local optimization quality depended on insert position. fixed.
     - insertion of multiple species is now done independently (=unordered)
     - performance improved (esp. for many added species/big trees)
   * generally improved combine performance (using SSE)
   * generally reduced the number of performed combines (skipping many useless)
   * added function to randomize (parts of) the tree
   * warns about insufficient sequence data (e.g. as result of too restrictive filtering; #631)
   * fixed 'RESTORE' (crashed after deleting species from tree; #528)
   * corrected handling of dots ('.') while combining ancestor sequences
   * fixed a bunch of internal bugs (#620, #627, ...)
   * added species-info mode
 - DNA realigner
   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
     - correctly re-syncs after 'X' (if possible at all)
     - no longer fails for 'B' and 'Z'
     - accepts 3 or more consecutive IUPAC codes in DNA
   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
   * fixed several minor bugs
 - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO)
 - species selections (editor configurations):
   * visualisation of multiple selections in standard tree view (#658; example in database demo.arb)
   * order can be changed; each configuration has a comment
 - sequence import/export:
   * manage/edit/test import-/export-filter-definitions from inside ARB (#691)
   * import can store configuration of imported species (#607)
   * corrected EMBL export filter (numbers at seq.data)
 - Tree shading (#443)
   * according to values stored in database
   * according to given topology (useful when comparing topologies)
 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
 - ARB_EDIT4:
   * display selected database fields as flags (allowing to toggle their value; #261).
     Example use: easily mark sequence as "curated" after manually checking its alignment.
   * allow to load missing SAIs
   * "view differences" to a reference sequence:
      - customizable:
        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
        * case-sensitivity
        * ignore different gap-types
      - equal data also gets hidden in consensus
      - refresh differences of all displayed sequences, when data of selected sequences changes
      - change reference sequence using CTRL-R or automatically let it follow the cursor
      - added hotkey to toggle mode: CTRL-D
      - fixed minor bugs
   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
     - now both calculations are strictly consistent:
       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
     - added sliders to consensus definition windows
     - user defined consensus settings exchangable between both consensus setups
     - fixed and updated documentation
   * added species-info mode + database save
   * predefined SAI color translation for PVP
 - changes to SAI generation
   * MAX_FREQUENCY:
     - considers IUPAC ambiguity codes proportionally
     - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
   * POS_VAR_BY_PARSIMONY (PVP):
     - now (again) works with amino acid data
 - expand zombies in tree (unfold groups)
 - compare taxonomy (and mark differences; #651)
 - search&query for taxonomic groups (#652)
   - many search criteria (name, size, marked, nesting-level, ingroup-distance, ...)
   - search multiple trees, detect duplicate and missing groups
   - operations on found groups (delete, rename, fold, mark)
 - added concept of "inverse groups" (aka "keeled groups")
 - group transfer between trees:
   - penalties can be customized in detail
   - quality reports (to log and optionally to target name)
 - external (command line) aligners:
   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
   * no longer ask what to do with aligned sequence, just overwrite it
     - only warn about real sequence changes (so please do NOT ignore from now on!)
 - config-managers:
   * possibility to restore factory defaults
   * added comment field for configurations
   * added them throughout arb (#647)
 - added slide controls throughout arb (#656)
 - tree (display) options:
   * fine grained scaling
   * add threshold for visible support values
   * group display (shading, customizable counters, triangle clades, optimized name+bootstrap display position)
   * diagonal branch style
   * parent branch position
   * all options are now also supported by ARB_PARSIMONY
   * improved auto-jump; now also works for groups
   * added optional auto-unfolding (to selected group/species)
   * select group on fold/unfold/create/move/..
   * draw selected group in cursor-color
   * added keys for tree-traversal (moving selected species or group)
 - synchronized tree scrolling (#683)
 - colorsets were invalidated by generating new IDs (#660). fixed.
 - added alternate RAxML (DNA only; version 8.2.8)
   - multicore support (automatically activates recommended number of threads)
   - evaluation, optimization and extension of existing trees with RAxML
 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
 - ACI
   - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands
   - improved ACI debugging: more verbose tracing (console log accessible from inside ARB)
 - NDS optionally uses only visible definitions
 - Search&Query (sort results numerically, improved macro compatibility)
 - Species info (improved detachment, field selection + macro compatibility)
 - updated integrated documentation

Fixes for arb-6.0.5 (4 May 2016):

 - fixes for ubuntu 16.04 build

Fixes for arb-6.0.4 (2 May 2016):

 - fixes for OSX build (SIP, accepted compilers)

Fixes for arb-6.0.3 (19 Nov 2015):

 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)

Fixes for arb-6.0.2 (8 Aug 2014):

 - compile issues on Snow Leopard (OSX 10.6)
 - merge Debian security fix for CVE-2008-5378
 - small changes to build system for Debian
 - add desktop integration files

Fixes for arb-6.0.1 (22 Jul 2014):

 - arb_parsimony
   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
   - corrected branchlength calculation for "Add marked partial species"
   - dots were treated as gaps for protein sequences (now treated as 'X'; analog to DNA treating gaps as 'N'). thx to Yan Shi for detecting that problem!
 - print
   - preview failed (showed empty postscript file)
   - print to file now always saves in user home
 - raxml (import tree with bootstrap values)

Major changes for arb-6.0 (4 Jun 2014):

 - merge databases allows to
   - merge from an existing database into the database loaded in ARB_NT
   - merge to existing databases from the database loaded in ARB_NT
 - ARB can now
   - be restarted with another database and
   - a second instance of ARB can be opened
 - ARB_DIST
   - Detect clusters of species with similar sequences (OTUs)
   - allow automatic recalculation of matrix and/or tree whenever some parameter or
     data changes (only makes sense for smaller species sets)
   - extract distance matrix from tree
 - Rewrote chimera check. Allows filtering
 - added RNACMA (computes clusters of correlated positions)
 - PT-Server
   - changed behavior
     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
     - reports previously missing hits in joined genes
     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
       matches that go beyond the end of the sequence)
     - dots in the middle of the alignment act like the sequence ends there
     - minimum probe length reduced to 2 (was 6)
     - allow up to 50% of probe to mismatch
   - performance
     - optimized memory-estimation (will build in fewer passes)
     - uses any number of passes (not only 1, 5, 25, ...)
     - allows to define used memory by setting environment variable ARB_MEMORY
     - reduced memory needed to build/run ptserver (approx. 50%)
     - reduced size of indexfile (.pt) to ~50%
     - fast startup of existing ptservers
   - probe design
     - faster in many cases
     - allow to design probes of length 8 (previously 10)
     - allow to design probes with different lengths (specifying min/max length)
     - fixed number of outgroup hits reported when decreasing temperature
       (now each outgroup member only occurs once)
     - show possible reasons why no probes could be designed
   - probe match (allow any number of mismatches)
   - next relative search
     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
     - corrected and improved scaling of relative scores
     - more accurate scores (due to fixes in PT-Server; see below)
     - faster in many cases
   - show errors from ptserver build in ARB
 - fast-aligner
   - searches next-relatives based on selected column-block
   - align multiple column-blocks based on SAI
 - Rewrote alignment adaption during merge
 - Insert/delete columns using a SAI to define affected columns
 - ARB_EDIT4
   - improved support for using multiple edit-windows
   - smoother refreshes
   - tweaked ORF display
 - tree importer/exporter
   - ARBs extended newick format (with bootstrap values) handled more restrictive now
   - fixed several bugs; improved errors/warnings
 - consensus trees
   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
   - fixed NJ-bootstrapping (no longer drops species)
 - tree display
   - Show brackets on open groups (dendrogram tree only)
   - rewrote IRS (folded) display
   - fixed tree key-bindings (mark, fold, ...)
   - improved several tree-commands (move, rotate, spread, length, width)
 - added a branch analysis tool
   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
   - added leaf-distance analysis
 - other tree functionality
   - treelist sortable now
   - new beautify-tree modes (radial tree / according to other tree)
   - function to remove marked/zombies from ALL trees
   - create multifurcations (by branchlength/bootstrap limit)
   - toggle 100% bootstrap values
 - tweaked printing (interface, overlapping)
 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
 - probe design:
   - added LOAD to result window
 - automation
   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
   - arb_ntree can execute macro from command line
   - added "Never ask again" to modal question boxes (for better compatibility with macros)
   - a macro can be called for all marked species (once for each)
   - macros can be nested (i.e. can call other macros)
 - support for user-specific customization:
   - of GDE menus (in ~/.arb_prop/gde)
   - of import/export filters (in ~/.arb_prop/filter)
 - ACI (some new commands, bugfixes)
 - updated/added external tools:
   - added FastTree (version 2.1.7)
   - added MAFFT (version 7.055)
   - added MrBayes (version 3.2.1)
   - added MUSCLE (version 3.8.31)
   - added PHYML (2013/07/08; also kept old version 2.4.5)
   - added PROBCONS (version 1.12)
   - updated RAxML (version 7.7.2)
 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
 - Support for mouse-wheel
 - many unlisted bugfixes
 - many internal refactorings


Fixes for arb_5.5 (15 Nov 2012):

 * arb_5.4 was broken (several external tools missing)


Fixes for arb_5.4 (14 Nov 2012):

 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
 * fixed several compilation issues (OSX; recent distro releases)


Fixes for arb_5.3 (10 Nov 2011):

 - bugfixes
   - fixed wrong absolute/ecoli position reported for some designed probes
   - decompression error handling (pt-server build issues)
   - fixed 'codon_start' generated with wrong type
   - fixed a buffer overflow in ACI
   - report failures to write to /tmp
 - changes
   - markSpecies.pl:
     mark by accession number
     partial/ambiguous matches
 - internal fixes
   - compilation fixes for OSX
   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
   - removed obsolete dependency from libXp


Fixes for arb_5.2 (5 Sep 2010):

 - 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 (1 Oct 2009):

 - 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 (4 Sep 2009):

 - 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 (7 Dec 2007):

 - 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 (22 Aug 2003):

 - 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 (7 Nov 2001):

 - 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 (24 Jul 2001):

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