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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