ARB change logFixes for arb-6.0.6 (22 Aug 2016):
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fixes for gcc 6.1.0
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tested gcc 4.9.4 + 5.4.0
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Fixes for arb-6.0.5 (4 May 2016):
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fixes for ubuntu 16.04 build
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Fixes for arb-6.0.4 (2 May 2016):
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fixes for OSX build (SIP, accepted compilers)
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Fixes for arb-6.0.3 (19 Nov 2015):
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fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
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Fixes for arb-6.0.2 (8 Aug 2014):
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compile issues on Snow Leopard (OSX 10.6)
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merge Debian security fix for CVE-2008-5378
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small changes to build system for Debian
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add desktop integration files
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Fixes for arb-6.0.1 (22 Jul 2014):
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arb_parsimony
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skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
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corrected branchlength calculation for "Add marked partial species"
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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!
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print
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preview failed (showed empty postscript file)
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print to file now always saves in user home
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raxml (import tree with bootstrap values)
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Major changes for arb-6.0 (4 Jun 2014):
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merge databases allows to
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merge from an existing database into the database loaded in ARB_NT
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merge to existing databases from the database loaded in ARB_NT
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ARB can now
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be restarted with another database and
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a second instance of ARB can be opened
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ARB_DIST
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Detect clusters of species with similar sequences (OTUs)
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allow automatic recalculation of matrix and/or tree whenever some parameter or data changes (only makes sense for smaller species sets)
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extract distance matrix from tree
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Rewrote chimera check. Allows filtering
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added RNACMA (computes clusters of correlated positions)
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PT-Server
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changed behavior
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no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
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reports previously missing hits in joined genes
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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)
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dots in the middle of the alignment act like the sequence ends there
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minimum probe length reduced to 2 (was 6)
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allow up to 50% of probe to mismatch
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performance
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optimized memory-estimation (will build in fewer passes)
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uses any number of passes (not only 1, 5, 25, ...)
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allows to define used memory by setting environment variable ARB_MEMORY
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reduced memory needed to build/run ptserver (approx. 50%)
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reduced size of indexfile (.pt) to ~50%
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fast startup of existing ptservers
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probe design
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faster in many cases
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allow to design probes of length 8 (previously 10)
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allow to design probes with different lengths (specifying min/max length)
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fixed number of outgroup hits reported when decreasing temperature (now each outgroup member only occurs once)
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show possible reasons why no probes could be designed
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probe match (allow any number of mismatches)
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next relative search
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can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
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corrected and improved scaling of relative scores
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more accurate scores (due to fixes in PT-Server; see below)
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faster in many cases
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show errors from ptserver build in ARB
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fast-aligner
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searches next-relatives based on selected column-block
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align multiple column-blocks based on SAI
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Rewrote alignment adaption during merge
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Insert/delete columns using a SAI to define affected columns
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ARB_EDIT4
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improved support for using multiple edit-windows
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smoother refreshes
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tweaked ORF display
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tree importer/exporter
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ARBs extended newick format (with bootstrap values) handled more restrictive now
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fixed several bugs; improved errors/warnings
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consensus trees
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calculate from multiple existing trees (also allows to merge not completely overlapping trees)
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fixed NJ-bootstrapping (no longer drops species)
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tree display
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Show brackets on open groups (dendrogram tree only)
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rewrote IRS (folded) display
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fixed tree key-bindings (mark, fold, ...)
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improved several tree-commands (move, rotate, spread, length, width)
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added a branch analysis tool
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groups several functions previously availiable via menuitems (e.g. mark long branches, etc.)
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added leaf-distance analysis
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other tree functionality
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treelist sortable now
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new beautify-tree modes (radial tree / according to other tree)
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function to remove marked/zombies from ALL trees
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create multifurcations (by branchlength/bootstrap limit)
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toggle 100% bootstrap values
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tweaked printing (interface, overlapping)
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if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
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probe design:
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added LOAD to result window
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automation
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macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
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arb_ntree can execute macro from command line
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added "Never ask again" to modal question boxes (for better compatibility with macros)
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a macro can be called for all marked species (once for each)
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macros can be nested (i.e. can call other macros)
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support for user-specific customization:
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of GDE menus (in ~/.arb_prop/gde)
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of import/export filters (in ~/.arb_prop/filter)
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ACI (some new commands, bugfixes)
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updated/added external tools:
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added FastTree (version 2.1.7)
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added MAFFT (version 7.055)
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added MrBayes (version 3.2.1)
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added MUSCLE (version 3.8.31)
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added PHYML (2013/07/08; also kept old version 2.4.5)
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added PROBCONS (version 1.12)
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updated RAxML (version 7.7.2)
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load/save for window specific settings (e.g. allows to share parts of configuration with other users)
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Support for mouse-wheel
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many unlisted bugfixes
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many internal refactorings
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Fixes for arb_5.5 (15 Nov 2012):
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arb_5.4 was broken (several external tools missing)
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Fixes for arb_5.4 (14 Nov 2012):
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make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
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fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
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fixed several compilation issues (OSX; recent distro releases)
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Fixes for arb_5.3 (10 Nov 2011):
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bugfixes
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fixed wrong absolute/ecoli position reported for some designed probes
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decompression error handling (pt-server build issues)
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fixed 'codon_start' generated with wrong type
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fixed a buffer overflow in ACI
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report failures to write to /tmp
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changes
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markSpecies.pl: mark by accession number partial/ambiguous matches
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internal fixes
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compilation fixes for OSX
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some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
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removed obsolete dependency from libXp
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Fixes for arb_5.2 (5 Sep 2010):
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bugfixes
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quicksave did silently do nothing (especially not save anything) if an error occurred
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ARB_EDIT4: crashed when using config with MANY unknown species
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ARB_SECEDIT: crashed when trying to paint strand w/o any base
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ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
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changes
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ARB uses xdg-open to display web-pages
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internal fixes
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karmic koala (gcc 4.4.1)
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installation script
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arb build process uses xsltproc instead of sablotron
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Fixes for arb_5.1 (1 Oct 2009):
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fixed a bug in 'Create species from consensus' (created sequence was corrupted)
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fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
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updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
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fixed broken demo.arb
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Major changes for arb_5.00 (4 Sep 2009):
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ARB 64bit version
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new genome importer
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search for next relatives improved (normal search and fast-aligner)
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new parameters to precise search
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improved speed
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partial sequence reach normal scores
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search&query
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supports regular expressions and ACI
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track hit information
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result sorting
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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)
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multiple PT-servers may be used in parallel
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fixed multiprobe
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type-conversion for DB fields
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SILVA compatible import filters
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Newick tree export:
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optionally save in human-readable format (big)
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closer to newick standard format (quoting style, comment, special chars in data)
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Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
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Fixed sequence quality calculation
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Secondary structures for proteins (DSSP)
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Distance matrix (arb_dist): mark by distance to selected
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ARB core
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many bugfixes and improvements to reliability
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faster sorting (general speedup)
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improved sequence compression (avoid worse trees, better ratio)
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improved handling of temporary files (permission/removal)
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prints backtraces in userland
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regular expression are POSIX standard now
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macro record/playback
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fixed several bugs
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you need to re-record your old macros!
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GUI:
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disabled auto-focus, you need to click now
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auto-raise windows on access
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Minor things:
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Ubuntu: packet installation for ARB
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Fixed novice/expert mode
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Mark deep/degenerated branches
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Increased NDS entries
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up-to-date Mac port (thx to Matt Cottrell)
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Major changes in ARB 07.12.07org (7 Dec 2007):
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rewrote secondary structure editor
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Sequence quality check
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Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
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tweaked base frequency filter generation
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Normal export (not using readseq) improved:
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supports filters and gap removal
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optimized for big amount of data
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reworked export filters
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Display translation with different ORFs in EDIT4
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ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
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added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
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more compact display in EDIT4
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capable to use iso10646 fonts
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supports various gcc versions (2.95.3 - 4.1.1)
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fixed a bug in DB optimization (occurred when fields had bigger protection than current)
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Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses different color for size-limited circles; fixed xfig-export-bug
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Allows Branchlength <-> Bootstrap value transfer (lossy!)
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fixed several scaling bugs in "folded tree"-mode
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improved import-filter error-messages
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NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives several new possibilities:
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export taxonomy via 'Export NDS list'
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display taxonomy in Editor etc.
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display of cascaded taxonomies
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display taxonomy of tree_1 in tree_2
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allows to write taxonomy into database field of species
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compare taxonomies of two trees
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...
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ACI:
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many new ACI commands
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unified handling of binary ACI-operators
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tracing of ACI actions for debugging purpose
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ARB Neighbour joining:
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bootstrap limit configurable
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bugfix: when aborting bootstrap calculation, sometimes no tree was generated
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EDIT4:
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added unalign right (block-op)
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added 'Save loaded properties'
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GENE MAP:
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multiple views possible at the same time
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origin now at "12 o'clock"
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implemented 'jump to gene'
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tweaked file selection
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Enhanced Search Depth for Probe Match --> max 20 MM
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CLUSTALW:
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separated menus for fast and slow alignment
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most parameters accessible from inside ARB now
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upgraded to PHYLIP 3.6 (adds PROML)
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external programs may be called parallel (e.g. several treeing programs)
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fixed bugs in protml and integration of protml
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rewrote ASCII database import
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arb_repair for databases of any size (script for database repair)
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fixed bug in data compression
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increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
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ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
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GDE menus cleanup
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translation/re-alignment tweaked
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unalign right (EDIT4)
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visualization of SAIs in Probe Match Results
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changed formatting of probe match results; increase # of allowed matches to 100.000; warn if results are truncated
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PT server for genes
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Probe design performance optimized
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fixed NEXUS export format
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exports group names into Newick format
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import XML tree files
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help for external tools now properly shown inside ARB
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Major changes in Beta 2003_08_22 (22 Aug 2003):
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automatic formatting of alignments
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SECEDIT may use EDIT4 colors
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fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
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updated clustalw to version 1.83
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Restore window sizes for ALL windows (too small sizes are ignored)
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new algorithm to add partial sequences to an existing tree
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PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
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Top area of ARB_NTREE may be reduced to maximize display area
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All arb menus may be detached (click dashed line at top of menu)
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visualization of SAIs (as background color behind Sequences)
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ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
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PT-server occupies more memory => does less passes; more diagnostic output
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small changes to status window (unhide behavior/time estimation)
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menus and menu-hotkeys reorganized
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colored buttons in color config windows
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alignment concatenation (e.g. several different genes)
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merging data of similar species (according selected database field)
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keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
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expanded sellists
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save/load fixed for multi probes
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Binary SAIs are editable in ARB_EDIT4
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Information windows are detachable (allows to have multiple windows showing different items)
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Scanning for hidden/unknown database fields improved and separated; possibility to remove unused fields.
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new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
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updated fastDNAml to 1.2.2
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added AxML (accelerated fastDNAml 1.2.2)
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Field transfer definitions for exporting gene-species
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File Selection: - recursive search available
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The ARB_NTREE macro recording/execution has been fixed
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Colorize species (see demo.arb)
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Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
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'IslandHopper' -- a new integrated aligner (beta)
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Many improvements and bugfixes to secondary structure editor:
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highlighting of search (i.e for probes) like in EDIT4
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interactive constraint editing (stretch/compress)
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probe info
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editing secondary structure in XFIG now possible
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visualization of SAIs
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import reads Unix, DOS, and MAC linefeeds
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NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
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tree and sequence export to XML ( DTDs are provided in ./lib/dtd ) (reloading of these XML files is planned for the future)
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fixed problems with phylip-tree import/export (bootstrap values,comments,...)
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search in all database fields possible ('[all fields]')
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up to 10 quicksaves are kept
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new ACI functions: upper, lower, caps, eval
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variables for import filter programming
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extract gene-species: creates acc; extraction to existing alignments
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sequence of selected gene is mirrored in ARB_EDIT4/local_signature (=> selected gene can be highlighted in primary editor)
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PCR primer-design for single genes
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when selecting a gene, the corresponding gene-species is selected (if found)
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save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
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file selection box in import window
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mark item with double click works in all search&query windows
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User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
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Fixed command line help for all Arb-modules
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Fixed problem parsing fonts (should fix display problems with default fonts)
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Mark mode now works in list-view as well (ARB_NTREE)
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Fixed appearance of 'tiny little boxes' (everywhere)
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Redesign of ARB help:
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a HTML version is in $ARBHOME/lib/help_html
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a text version is in $ARBHOME/lib/help (like before, but now generated)
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Major changes in Beta 2001_11_07 (7 Nov 2001):
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design probes to maximum length of 60 nucleotides
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fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
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import default changed to foreign data format, ali name '16s'
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printing of multi-page-trees works again
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implemented user defineable masks to access database fields
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fixed bugs in pt-server (lockup, unknown species just after building pt-server)
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improved performance during pt-server-build
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several programs coming along with ARB where updated (PHYLIP,...)
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reads EMBL genom files
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support for experiments (genom databases only)
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Major changes in Beta 2001_07_24 (24 Jul 2001):
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basic support for genoms (Gene Map, reads Genebank files)
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ported to libc6
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