source: trunk/arb_CHANGES.txt

Last change on this file was 19393, checked in by westram, 13 months ago
  • reintegrates 'ali' into 'trunk'
    • refactored misused enum
    • support for helix pairs:
      • drop non-standard defs
      • add more user defs
    • change defaults
    • add several predefined configs (esp. for IUPAC ambiguity codes)
  • adds: log:branches/ali@19376:19392
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 26.7 KB
Line 
1ARB change log
2
3Major changes for next release:
4
5 - tweaked 'Helix settings' in EDIT4
6   - defaults changed for GG ('#'->'='), TT + UU ('+'->'#'), ambiguity codes (''->'%')
7   - added several predefined configs (traditional, two handling ambiguity codes)
8 - detect poorly aligned helical regions in editor (#854)
9 - include SINA (1.7.2 patched)
10   - interface auto-adapts to sina version (still compatible with 1.3; currently needs patched version for 1.7.2)
11   - added script arb_sina_install_from_fat_tarball.sh (allows to install sina from fat-tarballs provided via arb homepage)
12 - split alignments (#846)
13 - tweaked progress
14   - better estimation for NJ, ConsensusTree, matrix calculation + PVP
15   - support for longer periods; prefer overestimation
16   - log to console (estimates finish)
17 - FastTree
18   - added support for protein sequences.
19   - customizable from GUI (rate categories, NJ, bootstraps).
20   - upgraded to version 2.1.11
21   - arb now provides single+multi processor versions of FastTree
22 - NDS (Node display setup)
23   - specifying a zero WIDTH now means "unlimited" (backward compatibel).
24   - avoid unwanted truncation (NDS-export, saved distance matrix).
25   - tree/export (using NDS)
26     - no longer truncates labels.
27     - group-labels are generated by NDS now.
28     - raise an error if non-ASCII characters are used in label (optionally).
29
30Fixes for arb-7.0.1 (31 Jan 2022):
31
32 - fix perl compatibility for macOS 12
33
34Major changes for arb-7.0 (1 Sep 2021):
35
36 - (Note: Details about ticket numbers (#NUM) specified below can be viewed at http://bugs.arb-home.de/ticket/NUM)
37 - ARB PARSIMONY
38   * topology optimization
39     - now (by default) strictly restricted to marked/visible parts of the tree (#640)
40     - restriction now customizable (marked/all; visible/all)
41     - tree costs for protein-data were not independent from root-position (as expected by model; #633).
42       Caused infinite running optimization under some circumstances.
43     - optimize-modes now strictly restrict to clicked subtrees. single/repeated optimization possible.
44     - KL-optimizer
45       * static path reduction slightly changed meaning. changed default settings.
46       * removed randomness (was just covering some bugs)
47       * improved general optimization speed
48   * branchlength calculation
49     - "forgot" to recalculate lengths under some conditions. fixed.
50     - is now independent of tree-root position (#641)
51   * adding species
52     - 'add partial species' failed if two partial species had NO overlap (#609). fixed.
53     - in 'add species + NNI' local optimization quality depended on insert position. fixed.
54     - insertion of multiple species is now done independently (=unordered; #643)
55     - performance improved (esp. for many added species/big trees; #643)
56   * generally improved combine performance (using SSE)
57   * generally reduced the number of performed combines (skipping many useless)
58   * added function to randomize (parts of) the tree
59   * warns about insufficient sequence data (e.g. as result of too restrictive filtering; #631)
60   * fixed 'RESTORE' (crashed after deleting species from tree; #528)
61   * corrected handling of dots ('.') while combining ancestor sequences
62   * fixed a bunch of internal bugs (#620, #627, #645, ...)
63   * added species-info mode
64 - added missing translation tables (genetic codes 24-31)
65 - added amino acid code Xle(=J), which means Ile(=I) or Leu(=L)
66 - DNA realigner
67   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
68     - correctly re-syncs after 'X' (if possible at all)
69     - no longer fails for 'B', 'J' and 'Z'
70     - accepts 3 or more consecutive IUPAC codes in DNA
71   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
72   * fixed several minor bugs (#563,..)
73 - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO)
74 - species selections (editor configurations):
75   * visualisation of multiple selections in standard tree view (#658; example in database demo.arb)
76   * order can be changed; each configuration has a comment
77 - import/export (species,sequence):
78   * manage/edit/test import-/export-filter-definitions from inside ARB (#691)
79   * import can store configuration of imported species (#607)
80   * field transfer sets (#562) may be used to customize import/export behavior (also usable from arb merge-tool)
81   * corrected EMBL export filter (numbers at seq.data; #638)
82   * detected duplicates no longer abort complete import (#779)
83   * new CLI sequence exporter 'arb_export_seq_filtered' (#743)
84 - Tree shading (#443)
85   * according to values stored in database
86   * according to given topology (useful when comparing topologies)
87   * added customisable color ranges (#682)
88 - support for extra database compression (using gzip, bzip2, xz; #665); databases cannot be opened by versions before arb-7.0
89 - ARB_EDIT4:
90   * display selected database fields as flags (allowing to toggle their value; #261).
91     Example use: easily mark sequence as "curated" after manually checking its alignment.
92   * allow to load missing SAIs
93   * "view differences" to a reference sequence:
94      - customizable:
95        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
96        * case-sensitivity
97        * ignore different gap-types
98      - equal data also gets hidden in consensus
99      - refresh differences of all displayed sequences, when data of selected sequences changes
100      - change reference sequence using CTRL-R or automatically let it follow the cursor
101      - added hotkey to toggle mode: CTRL-D
102      - fixed minor bugs
103   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
104     - now both calculations are strictly consistent (#663):
105       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
106       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
107     - added sliders to consensus definition windows
108     - user defined consensus settings exchangable between both consensus setups
109     - fixed and updated documentation
110   * added species-info mode + database save (#52,#362)
111   * predefined SAI color translation for PVP
112 - changes to SAI generation
113   * MAX_FREQUENCY:
114     - considers IUPAC ambiguity codes proportionally
115     - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
116   * POS_VAR_BY_PARSIMONY (PVP):
117     - now (again) works with amino acid data (#782)
118     - added CLI tool 'arb_calc_pvp' (#701)
119   * implemented a SAI calculator (allows to modify or combine multiple SAIs)
120 - expand zombies in tree (unfold groups; #22)
121 - compare taxonomy (and mark differences; #651)
122 - search&query for taxonomic groups (#652)
123   - many search criteria (name, size, marked, nesting-level, ingroup-distance (#653), ...)
124   - search multiple trees, detect duplicate and missing groups
125   - operations on found groups (delete, rename, fold, mark)
126 - added concept of "inverse groups" (aka "keeled groups"; #735)
127 - group transfer between trees (#780):
128   - penalties can be customized in detail
129   - quality reports (to log and optionally to target name)
130 - synchronize positions of roots of multiple trees (#449)
131 - external (command line) aligners (#504):
132   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
133   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
134   * no longer ask what to do with aligned sequence, just overwrite it
135     - only warn about real sequence changes (so please do NOT ignore from now on!)
136 - config-managers:
137   * possibility to restore factory defaults
138   * added comment field for configurations
139   * added them throughout arb (#647)
140 - added slide controls throughout arb (#656)
141 - tree (display) options:
142   * fine grained scaling
143   * group display (shading, customizable counters (#118,#209), triangle clades, name display position)
144   * bootstrap values (filter by upper/lower limits, display position/styles, on/off toggle; #614)
145   * diagonal branch style (#578)
146   * parent branch position
147   * all options are now also supported by ARB_PARSIMONY
148   * improved auto-jump; now also works for groups
149   * added optional auto-unfolding (to selected group/species)
150   * select group on fold/unfold/create/move/..
151   * draw selected group in cursor-color (#709)
152   * added keys for tree-traversal (moving to selected species or group; #687)
153 - synchronized tree scrolling (#683)
154 - colorsets were invalidated by generating new IDs (#660). fixed.
155 - added alternate RAxML (DNA only; version 8.2.8)
156   - multicore support (automatically activates recommended number of threads)
157   - evaluation, optimization and extension of existing trees with RAxML (#681)
158 - fix performance of
159   * "format sequences" (broken in arb-6.0.x series; #702)
160   * nameserver for huge databases (#646)
161   * closing arb (if database uses fastload file; #649)
162 - ACI
163   - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands
164   - allow access to other species via ID or accession number (findspec, ...)
165   - improved ACI debugging: more verbose tracing (console log accessible from inside ARB)
166 - NDS optionally uses only visible definitions
167 - Search&Query:
168   * sort results numerically (#203)
169   * recursive search through all fields (#773)
170 - Species information window: improved detachment, field selection (#695)
171 - improved macro compatibility:
172   * check compatibility with installed perl version during arb startup (#754)
173   * esp. tweaked compatibility of 'Search&Query' and 'Species information window'
174   * fixed a lot of internal names (missing or duplicated) which are used for macros (#429)
175 - improved OSX compatibility (thx to Jan Gerken)
176 - updated integrated documentation (#409)
177
178
179Fixes for arb-6.0.6 (22 Aug 2016):
180
181 - fixes for gcc 6.1.0
182 - tested gcc 4.9.4 + 5.4.0
183
184Fixes for arb-6.0.5 (4 May 2016):
185
186 - fixes for ubuntu 16.04 build
187
188Fixes for arb-6.0.4 (2 May 2016):
189
190 - fixes for OSX build (SIP, accepted compilers)
191
192Fixes for arb-6.0.3 (19 Nov 2015):
193
194 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
195
196Fixes for arb-6.0.2 (8 Aug 2014):
197
198 - compile issues on Snow Leopard (OSX 10.6)
199 - merge Debian security fix for CVE-2008-5378
200 - small changes to build system for Debian
201 - add desktop integration files
202
203Fixes for arb-6.0.1 (22 Jul 2014):
204
205 - arb_parsimony
206   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
207   - corrected branchlength calculation for "Add marked partial species"
208   - dots were treated as gaps for protein sequences (now treated as 'X'; analog to DNA treating gaps as 'N'; #144). thx to Yan Shi for detecting that problem!
209 - print
210   - preview failed (showed empty postscript file)
211   - print to file now always saves in user home
212 - raxml (import tree with bootstrap values)
213
214Major changes for arb-6.0 (4 Jun 2014):
215
216 - merge databases allows to
217   - merge from an existing database into the database loaded in ARB_NT
218   - merge to existing databases from the database loaded in ARB_NT
219 - ARB can now
220   - be restarted with another database and
221   - a second instance of ARB can be opened
222 - ARB_DIST
223   - Detect clusters of species with similar sequences (OTUs)
224   - allow automatic recalculation of matrix and/or tree whenever some parameter or
225     data changes (only makes sense for smaller species sets)
226   - extract distance matrix from tree
227 - Rewrote chimera check. Allows filtering
228 - added RNACMA (computes clusters of correlated positions)
229 - PT-Server
230   - changed behavior
231     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
232     - reports previously missing hits in joined genes
233     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
234       matches that go beyond the end of the sequence)
235     - dots in the middle of the alignment act like the sequence ends there
236     - minimum probe length reduced to 2 (was 6)
237     - allow up to 50% of probe to mismatch
238   - performance
239     - optimized memory-estimation (will build in fewer passes)
240     - uses any number of passes (not only 1, 5, 25, ...)
241     - allows to define used memory by setting environment variable ARB_MEMORY
242     - reduced memory needed to build/run ptserver (approx. 50%)
243     - reduced size of indexfile (.pt) to ~50%
244     - fast startup of existing ptservers
245   - probe design
246     - faster in many cases
247     - allow to design probes of length 8 (previously 10)
248     - allow to design probes with different lengths (specifying min/max length)
249     - fixed number of outgroup hits reported when decreasing temperature
250       (now each outgroup member only occurs once)
251     - show possible reasons why no probes could be designed
252   - probe match (allow any number of mismatches)
253   - next relative search
254     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
255     - corrected and improved scaling of relative scores
256     - more accurate scores (due to fixes in PT-Server; see below)
257     - faster in many cases
258   - show errors from ptserver build in ARB
259 - fast-aligner
260   - searches next-relatives based on selected column-block
261   - align multiple column-blocks based on SAI
262 - Rewrote alignment adaption during merge
263 - Insert/delete columns using a SAI to define affected columns
264 - ARB_EDIT4
265   - improved support for using multiple edit-windows
266   - smoother refreshes
267   - tweaked ORF display
268 - tree importer/exporter
269   - ARBs extended newick format (with bootstrap values) handled more restrictive now
270   - fixed several bugs; improved errors/warnings
271 - consensus trees
272   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
273   - fixed NJ-bootstrapping (no longer drops species)
274 - tree display
275   - Show brackets on open groups (dendrogram tree only)
276   - rewrote IRS (folded) display
277   - fixed tree key-bindings (mark, fold, ...)
278   - improved several tree-commands (move, rotate, spread, length, width)
279 - added a branch analysis tool
280   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
281   - added leaf-distance analysis
282 - other tree functionality
283   - treelist sortable now
284   - new beautify-tree modes (radial tree / according to other tree)
285   - function to remove marked/zombies from ALL trees
286   - create multifurcations (by branchlength/bootstrap limit)
287   - toggle 100% bootstrap values
288 - tweaked printing (interface, overlapping)
289 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
290 - probe design:
291   - added LOAD to result window
292 - automation
293   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
294   - arb_ntree can execute macro from command line
295   - added "Never ask again" to modal question boxes (for better compatibility with macros)
296   - a macro can be called for all marked species (once for each)
297   - macros can be nested (i.e. can call other macros)
298 - support for user-specific customization:
299   - of GDE menus (in ~/.arb_prop/gde)
300   - of import/export filters (in ~/.arb_prop/filter)
301 - ACI (some new commands, bugfixes)
302 - updated/added external tools:
303   - added FastTree (version 2.1.7)
304   - added MAFFT (version 7.055)
305   - added MrBayes (version 3.2.1)
306   - added MUSCLE (version 3.8.31)
307   - added PHYML (2013/07/08; also kept old version 2.4.5)
308   - added PROBCONS (version 1.12)
309   - updated RAxML (version 7.7.2)
310 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
311 - Support for mouse-wheel
312 - many unlisted bugfixes
313 - many internal refactorings
314
315
316Fixes for arb_5.5 (15 Nov 2012):
317
318 * arb_5.4 was broken (several external tools missing)
319
320
321Fixes for arb_5.4 (14 Nov 2012):
322
323 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
324 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
325 * fixed several compilation issues (OSX; recent distro releases)
326
327
328Fixes for arb_5.3 (10 Nov 2011):
329
330 - bugfixes
331   - fixed wrong absolute/ecoli position reported for some designed probes
332   - decompression error handling (pt-server build issues)
333   - fixed 'codon_start' generated with wrong type
334   - fixed a buffer overflow in ACI
335   - report failures to write to /tmp
336 - changes
337   - markSpecies.pl:
338     mark by accession number
339     partial/ambiguous matches
340 - internal fixes
341   - compilation fixes for OSX
342   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
343   - removed obsolete dependency from libXp
344
345
346Fixes for arb_5.2 (5 Sep 2010):
347
348 - bugfixes
349   - quicksave did silently do nothing (especially not save anything) if an error occurred
350   - ARB_EDIT4: crashed when using config with MANY unknown species
351   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
352   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
353 - changes
354   - ARB uses xdg-open to display web-pages
355 - internal fixes
356   - karmic koala (gcc 4.4.1)
357   - installation script
358   - arb build process uses xsltproc instead of sablotron
359
360
361Fixes for arb_5.1 (1 Oct 2009):
362
363 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
364 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
365 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
366 - fixed broken demo.arb
367
368
369Major changes for arb_5.00 (4 Sep 2009):
370
371 - ARB 64bit version
372 - new genome importer
373 - search for next relatives improved (normal search and fast-aligner)
374   - new parameters to precise search
375   - improved speed
376   - partial sequence reach normal scores
377 - search&query
378   - supports regular expressions and ACI
379   - track hit information
380   - result sorting
381 - Nameservers with add.field have to be started with default value
382   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
383 - multiple PT-servers may be used in parallel
384 - fixed multiprobe
385 - type-conversion for DB fields
386 - SILVA compatible import filters
387 - Newick tree export:
388   - optionally save in human-readable format (big)
389   - closer to newick standard format (quoting style, comment, special chars in data)
390 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
391 - Fixed sequence quality calculation
392 - Secondary structures for proteins (DSSP)
393 - Distance matrix (arb_dist): mark by distance to selected
394 - ARB core
395   - many bugfixes and improvements to reliability
396   - faster sorting (general speedup)
397   - improved sequence compression (avoid worse trees, better ratio)
398   - improved handling of temporary files (permission/removal)
399   - prints backtraces in userland
400   - regular expression are POSIX standard now
401 - macro record/playback
402   - fixed several bugs
403   - you need to re-record your old macros!
404 - GUI:
405   - disabled auto-focus, you need to click now
406   - auto-raise windows on access
407 - Minor things:
408   - Ubuntu: packet installation for ARB
409   - Fixed novice/expert mode
410   - Mark deep/degenerated branches
411   - Increased NDS entries
412 - up-to-date Mac port (thx to Matt Cottrell)
413
414Major changes in ARB 07.12.07org (7 Dec 2007):
415
416 - rewrote secondary structure editor
417 - Sequence quality check
418 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
419 - tweaked base frequency filter generation
420 - Normal export (not using readseq) improved:
421   - supports filters and gap removal
422   - optimized for big amount of data
423   - reworked export filters
424 - Display translation with different ORFs in EDIT4
425 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
426 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
427 - more compact display in EDIT4
428 - capable to use iso10646 fonts
429 - supports various gcc versions (2.95.3 - 4.1.1)
430 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
431 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
432   different color for size-limited circles; fixed xfig-export-bug
433 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
434 - fixed several scaling bugs in "folded tree"-mode
435 - improved import-filter error-messages
436 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
437   several new possibilities:
438   - export taxonomy via 'Export NDS list'
439   - display taxonomy in Editor etc.
440   - display of cascaded taxonomies
441   - display taxonomy of tree_1 in tree_2
442   - allows to write taxonomy into database field of species
443   - compare taxonomies of two trees
444   - ...
445 - ACI:
446   - many new ACI commands
447   - unified handling of binary ACI-operators
448   - tracing of ACI actions for debugging purpose
449 - ARB Neighbour joining:
450   - bootstrap limit configurable
451   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
452 - EDIT4:
453   - added unalign right (block-op)
454   - added 'Save loaded properties'
455 - GENE MAP:
456   - multiple views possible at the same time
457   - origin now at "12 o'clock"
458   - implemented 'jump to gene'
459 - tweaked file selection
460 - Enhanced Search Depth for Probe Match --> max 20 MM
461 - CLUSTALW:
462   - separated menus for fast and slow alignment
463   - most parameters accessible from inside ARB now
464 - upgraded to PHYLIP 3.6 (adds PROML)
465 - external programs may be called parallel (e.g. several treeing programs)
466 - fixed bugs in protml and integration of protml
467 - rewrote ASCII database import
468 - arb_repair for databases of any size (script for database repair)
469 - fixed bug in data compression
470 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
471 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
472 - GDE menus cleanup
473 - translation/re-alignment tweaked
474 - unalign right (EDIT4)
475 - visualization of SAIs in Probe Match Results
476 - changed formatting of probe match results; increase # of allowed matches to 100.000;
477   warn if results are truncated
478 - PT server for genes
479 - Probe design performance optimized
480 - fixed NEXUS export format
481 - exports group names into Newick format
482 - import XML tree files
483 - help for external tools now properly shown inside ARB
484
485Major changes in Beta 2003_08_22 (22 Aug 2003):
486
487 - automatic formatting of alignments
488 - SECEDIT may use EDIT4 colors
489 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
490 - updated clustalw to version 1.83
491 - Restore window sizes for ALL windows (too small sizes are ignored)
492 - new algorithm to add partial sequences to an existing tree
493 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
494 - Top area of ARB_NTREE may be reduced to maximize display area
495 - All arb menus may be detached (click dashed line at top of menu)
496 - visualization of SAIs (as background color behind Sequences)
497 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
498 - PT-server occupies more memory => does less passes; more diagnostic output
499 - small changes to status window (unhide behavior/time estimation)
500 - menus and menu-hotkeys reorganized
501 - colored buttons in color config windows
502 - alignment concatenation (e.g. several different genes)
503 - merging data of similar species (according selected database field)
504 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
505 - expanded sellists
506 - save/load fixed for multi probes
507 - Binary SAIs are editable in ARB_EDIT4
508 - Information windows are detachable (allows to have multiple windows showing different items)
509 - Scanning for hidden/unknown database fields improved and separated;
510   possibility to remove unused fields.
511 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
512 - updated fastDNAml to 1.2.2
513 - added AxML (accelerated fastDNAml 1.2.2)
514 - Field transfer definitions for exporting gene-species
515 - File Selection: - recursive search available
516 - The ARB_NTREE macro recording/execution has been fixed
517 - Colorize species (see demo.arb)
518 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
519 - 'IslandHopper' -- a new integrated aligner (beta)
520 - Many improvements and bugfixes to secondary structure editor:
521   - highlighting of search (i.e for probes) like in EDIT4
522   - interactive constraint editing (stretch/compress)
523   - probe info
524   - editing secondary structure in XFIG now possible
525   - visualization of SAIs
526 - import reads Unix, DOS, and MAC linefeeds
527 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
528 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
529   (reloading of these XML files is planned for the future)
530 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
531 - search in all database fields possible ('[all fields]')
532 - up to 10 quicksaves are kept
533 - new ACI functions: upper, lower, caps, eval
534 - variables for import filter programming
535 - extract gene-species: creates acc; extraction to existing alignments
536 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
537   (=> selected gene can be highlighted in primary editor)
538 - PCR primer-design for single genes
539 - when selecting a gene, the corresponding gene-species is selected (if found)
540 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
541 - file selection box in import window
542 - mark item with double click works in all search&query windows
543 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
544 - Fixed command line help for all Arb-modules
545 - Fixed problem parsing fonts (should fix display problems with default fonts)
546 - Mark mode now works in list-view as well (ARB_NTREE)
547 - Fixed appearance of 'tiny little boxes' (everywhere)
548 - Redesign of ARB help:
549     - a HTML version is in $ARBHOME/lib/help_html
550     - a text version is in $ARBHOME/lib/help (like before, but now generated)
551
552Major changes in Beta 2001_11_07 (7 Nov 2001):
553
554 - design probes to maximum length of 60 nucleotides
555 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
556 - import default changed to foreign data format, ali name '16s'
557 - printing of multi-page-trees works again
558 - implemented user defineable masks to access database fields
559 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
560 - improved performance during pt-server-build
561 - several programs coming along with ARB where updated (PHYLIP,...)
562 - reads EMBL genom files
563 - support for experiments (genom databases only)
564
565Major changes in Beta 2001_07_24 (24 Jul 2001):
566
567 - basic support for genoms (Gene Map, reads Genebank files)
568 - ported to libc6
569
570Changes in ancient versions (last century):
571
572 - see http://help.arb-home.de/version.html
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