ARB change log Major changes for arb_5.00: - 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: - 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: - 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: - 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: - basic support for genoms (Gene Map, reads Genebank files) - ported to libc6