| More docs on the ARB website. See also index of helppages. Last update on 27. Jun 2017 .

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- ARB: a Short Introduction
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# ARB change log

- Fixes for arb-6.0.6 (22 Aug 2016):
- Fixes for arb-6.0.5 (4 May 2016):
- Fixes for arb-6.0.4 (2 May 2016):
- Fixes for arb-6.0.3 (19 Nov 2015):
- Fixes for arb-6.0.2 (8 Aug 2014):
- Fixes for arb-6.0.1 (22 Jul 2014):
- Major changes for arb-6.0 (4 Jun 2014):
- Fixes for arb_5.5 (15 Nov 2012):
- Fixes for arb_5.4 (14 Nov 2012):
- Fixes for arb_5.3 (10 Nov 2011):
- Fixes for arb_5.2 (5 Sep 2010):
- Fixes for arb_5.1 (1 Oct 2009):
- Major changes for arb_5.00 (4 Sep 2009):
- Major changes in ARB 07.12.07org (7 Dec 2007):
- Major changes in Beta 2003_08_22 (22 Aug 2003):
- Major changes in Beta 2001_11_07 (7 Nov 2001):
- Major changes in Beta 2001_07_24 (24 Jul 2001):

## Fixes for arb-6.0.6 (22 Aug 2016):

- fixes for gcc 6.1.0
- tested gcc 4.9.4 + 5.4.0

## 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 availiable 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