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Last update on 04. Dec 2013 .
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ARB change log

Fixes for arb_5.5:

* arb_5.4 was broken (several external tools missing)

 

Fixes for arb_5.4:

* 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:

* 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:

* 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:

* 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:

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