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:
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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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