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Last update on 09. Aug 2017 .
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    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 anchestor 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; import stores configuration (#607)

    • 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

    • SAI: 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%)

    • expand zombies in tree (unfold groups)
    • compare taxonomy (and mark differences; #651)
    • search&query for taxonomic groups (#652)
    • 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)
    • updated integrated documentation

     

    Minor changes

    • corrected EMBL export filter (numbers at seq.data)
    • NDS optionally uses only visible definitions

     

    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