source: trunk/arb_CHANGES.txt

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1ARB change log
2
3Major changes for next release:
4
5 - ARB PARSIMONY
6   * topology optimization
7     - now (by default) strictly restricted to marked/visible parts of the tree (#640)
8     - restriction now customizable (marked/all; visible/all)
9     - tree costs for protein-data were not independent from root-position (as expected by model; #633).
10       Caused infinite running optimization under some circumstances.
11     - optimize-modes now strictly restrict to clicked subtrees. single/repeated optimization possible.
12     - KL-optimizer
13       * static path reduction slightly changed meaning. changed default settings.
14       * removed randomness (was just covering some bugs)
15       * improved general optimization speed
16   * branchlength calculation
17     - "forgot" to recalculate lengths under some conditions. fixed.
18     - is now independent of tree-root position (#641)
19   * adding species
20     - 'add partial species' failed if two partial species had NO overlap (#609). fixed.
21     - in 'add species + NNI' local optimization quality depended on insert position. fixed.
22     - insertion of multiple species is now done independently (=unordered)
23     - performance improved (esp. for many added species/big trees)
24   * generally improved combine performance (using SSE)
25   * generally reduced the number of performed combines (skipping many useless)
26   * added function to randomize (parts of) the tree
27   * warns about insufficient sequence data (e.g. as result of too restrictive filtering; #631)
28   * fixed 'RESTORE' (crashed after deleting species from tree; #528)
29   * corrected handling of dots ('.') while combining ancestor sequences
30   * fixed a bunch of internal bugs (#620, #627, ...)
31   * added species-info mode
32 - added missing translation tables (genetic codes 24-31)
33 - added amino acid code Xle(=J), which means Ile(=I) or Leu(=L)
34 - DNA realigner
35   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
36     - correctly re-syncs after 'X' (if possible at all)
37     - no longer fails for 'B', 'J' and 'Z'
38     - accepts 3 or more consecutive IUPAC codes in DNA
39   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
40   * fixed several minor bugs
41 - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO)
42 - species selections (editor configurations):
43   * visualisation of multiple selections in standard tree view (#658; example in database demo.arb)
44   * order can be changed; each configuration has a comment
45 - sequence import/export:
46   * manage/edit/test import-/export-filter-definitions from inside ARB (#691)
47   * import can store configuration of imported species (#607)
48   * corrected EMBL export filter (numbers at seq.data)
49 - Tree shading (#443)
50   * according to values stored in database
51   * according to given topology (useful when comparing topologies)
52 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
53 - ARB_EDIT4:
54   * display selected database fields as flags (allowing to toggle their value; #261).
55     Example use: easily mark sequence as "curated" after manually checking its alignment.
56   * allow to load missing SAIs
57   * "view differences" to a reference sequence:
58      - customizable:
59        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
60        * case-sensitivity
61        * ignore different gap-types
62      - equal data also gets hidden in consensus
63      - refresh differences of all displayed sequences, when data of selected sequences changes
64      - change reference sequence using CTRL-R or automatically let it follow the cursor
65      - added hotkey to toggle mode: CTRL-D
66      - fixed minor bugs
67   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
68     - now both calculations are strictly consistent:
69       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
70       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
71     - added sliders to consensus definition windows
72     - user defined consensus settings exchangable between both consensus setups
73     - fixed and updated documentation
74   * added species-info mode + database save
75   * predefined SAI color translation for PVP
76 - changes to SAI generation
77   * MAX_FREQUENCY:
78     - considers IUPAC ambiguity codes proportionally
79     - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
80   * POS_VAR_BY_PARSIMONY (PVP):
81     - now (again) works with amino acid data
82 - expand zombies in tree (unfold groups)
83 - compare taxonomy (and mark differences; #651)
84 - search&query for taxonomic groups (#652)
85   - many search criteria (name, size, marked, nesting-level, ingroup-distance, ...)
86   - search multiple trees, detect duplicate and missing groups
87   - operations on found groups (delete, rename, fold, mark)
88 - added concept of "inverse groups" (aka "keeled groups")
89 - group transfer between trees:
90   - penalties can be customized in detail
91   - quality reports (to log and optionally to target name)
92 - external (command line) aligners:
93   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
94   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
95   * no longer ask what to do with aligned sequence, just overwrite it
96     - only warn about real sequence changes (so please do NOT ignore from now on!)
97 - config-managers:
98   * possibility to restore factory defaults
99   * added comment field for configurations
100   * added them throughout arb (#647)
101 - added slide controls throughout arb (#656)
102 - tree (display) options:
103   * fine grained scaling
104   * add threshold for visible support values
105   * group display (shading, customizable counters, triangle clades, name display position)
106   * bootstrap values (filter by upper/lower limits, display position/styles, on/off toggle)
107   * diagonal branch style
108   * parent branch position
109   * all options are now also supported by ARB_PARSIMONY
110   * improved auto-jump; now also works for groups
111   * added optional auto-unfolding (to selected group/species)
112   * select group on fold/unfold/create/move/..
113   * draw selected group in cursor-color
114   * added keys for tree-traversal (moving selected species or group)
115 - synchronized tree scrolling (#683)
116 - colorsets were invalidated by generating new IDs (#660). fixed.
117 - added alternate RAxML (DNA only; version 8.2.8)
118   - multicore support (automatically activates recommended number of threads)
119   - evaluation, optimization and extension of existing trees with RAxML
120 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
121 - ACI
122   - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands
123   - improved ACI debugging: more verbose tracing (console log accessible from inside ARB)
124 - NDS optionally uses only visible definitions
125 - Search&Query (sort results numerically, improved macro compatibility)
126 - Species info (improved detachment, field selection + macro compatibility)
127 - updated integrated documentation
128
129Fixes for arb-6.0.5 (4 May 2016):
130
131 - fixes for ubuntu 16.04 build
132
133Fixes for arb-6.0.4 (2 May 2016):
134
135 - fixes for OSX build (SIP, accepted compilers)
136
137Fixes for arb-6.0.3 (19 Nov 2015):
138
139 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
140
141Fixes for arb-6.0.2 (8 Aug 2014):
142
143 - compile issues on Snow Leopard (OSX 10.6)
144 - merge Debian security fix for CVE-2008-5378
145 - small changes to build system for Debian
146 - add desktop integration files
147
148Fixes for arb-6.0.1 (22 Jul 2014):
149
150 - arb_parsimony
151   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
152   - corrected branchlength calculation for "Add marked partial species"
153   - 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!
154 - print
155   - preview failed (showed empty postscript file)
156   - print to file now always saves in user home
157 - raxml (import tree with bootstrap values)
158
159Major changes for arb-6.0 (4 Jun 2014):
160
161 - merge databases allows to
162   - merge from an existing database into the database loaded in ARB_NT
163   - merge to existing databases from the database loaded in ARB_NT
164 - ARB can now
165   - be restarted with another database and
166   - a second instance of ARB can be opened
167 - ARB_DIST
168   - Detect clusters of species with similar sequences (OTUs)
169   - allow automatic recalculation of matrix and/or tree whenever some parameter or
170     data changes (only makes sense for smaller species sets)
171   - extract distance matrix from tree
172 - Rewrote chimera check. Allows filtering
173 - added RNACMA (computes clusters of correlated positions)
174 - PT-Server
175   - changed behavior
176     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
177     - reports previously missing hits in joined genes
178     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
179       matches that go beyond the end of the sequence)
180     - dots in the middle of the alignment act like the sequence ends there
181     - minimum probe length reduced to 2 (was 6)
182     - allow up to 50% of probe to mismatch
183   - performance
184     - optimized memory-estimation (will build in fewer passes)
185     - uses any number of passes (not only 1, 5, 25, ...)
186     - allows to define used memory by setting environment variable ARB_MEMORY
187     - reduced memory needed to build/run ptserver (approx. 50%)
188     - reduced size of indexfile (.pt) to ~50%
189     - fast startup of existing ptservers
190   - probe design
191     - faster in many cases
192     - allow to design probes of length 8 (previously 10)
193     - allow to design probes with different lengths (specifying min/max length)
194     - fixed number of outgroup hits reported when decreasing temperature
195       (now each outgroup member only occurs once)
196     - show possible reasons why no probes could be designed
197   - probe match (allow any number of mismatches)
198   - next relative search
199     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
200     - corrected and improved scaling of relative scores
201     - more accurate scores (due to fixes in PT-Server; see below)
202     - faster in many cases
203   - show errors from ptserver build in ARB
204 - fast-aligner
205   - searches next-relatives based on selected column-block
206   - align multiple column-blocks based on SAI
207 - Rewrote alignment adaption during merge
208 - Insert/delete columns using a SAI to define affected columns
209 - ARB_EDIT4
210   - improved support for using multiple edit-windows
211   - smoother refreshes
212   - tweaked ORF display
213 - tree importer/exporter
214   - ARBs extended newick format (with bootstrap values) handled more restrictive now
215   - fixed several bugs; improved errors/warnings
216 - consensus trees
217   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
218   - fixed NJ-bootstrapping (no longer drops species)
219 - tree display
220   - Show brackets on open groups (dendrogram tree only)
221   - rewrote IRS (folded) display
222   - fixed tree key-bindings (mark, fold, ...)
223   - improved several tree-commands (move, rotate, spread, length, width)
224 - added a branch analysis tool
225   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
226   - added leaf-distance analysis
227 - other tree functionality
228   - treelist sortable now
229   - new beautify-tree modes (radial tree / according to other tree)
230   - function to remove marked/zombies from ALL trees
231   - create multifurcations (by branchlength/bootstrap limit)
232   - toggle 100% bootstrap values
233 - tweaked printing (interface, overlapping)
234 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
235 - probe design:
236   - added LOAD to result window
237 - automation
238   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
239   - arb_ntree can execute macro from command line
240   - added "Never ask again" to modal question boxes (for better compatibility with macros)
241   - a macro can be called for all marked species (once for each)
242   - macros can be nested (i.e. can call other macros)
243 - support for user-specific customization:
244   - of GDE menus (in ~/.arb_prop/gde)
245   - of import/export filters (in ~/.arb_prop/filter)
246 - ACI (some new commands, bugfixes)
247 - updated/added external tools:
248   - added FastTree (version 2.1.7)
249   - added MAFFT (version 7.055)
250   - added MrBayes (version 3.2.1)
251   - added MUSCLE (version 3.8.31)
252   - added PHYML (2013/07/08; also kept old version 2.4.5)
253   - added PROBCONS (version 1.12)
254   - updated RAxML (version 7.7.2)
255 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
256 - Support for mouse-wheel
257 - many unlisted bugfixes
258 - many internal refactorings
259
260
261Fixes for arb_5.5 (15 Nov 2012):
262
263 * arb_5.4 was broken (several external tools missing)
264
265
266Fixes for arb_5.4 (14 Nov 2012):
267
268 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
269 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
270 * fixed several compilation issues (OSX; recent distro releases)
271
272
273Fixes for arb_5.3 (10 Nov 2011):
274
275 - bugfixes
276   - fixed wrong absolute/ecoli position reported for some designed probes
277   - decompression error handling (pt-server build issues)
278   - fixed 'codon_start' generated with wrong type
279   - fixed a buffer overflow in ACI
280   - report failures to write to /tmp
281 - changes
282   - markSpecies.pl:
283     mark by accession number
284     partial/ambiguous matches
285 - internal fixes
286   - compilation fixes for OSX
287   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
288   - removed obsolete dependency from libXp
289
290
291Fixes for arb_5.2 (5 Sep 2010):
292
293 - bugfixes
294   - quicksave did silently do nothing (especially not save anything) if an error occurred
295   - ARB_EDIT4: crashed when using config with MANY unknown species
296   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
297   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
298 - changes
299   - ARB uses xdg-open to display web-pages
300 - internal fixes
301   - karmic koala (gcc 4.4.1)
302   - installation script
303   - arb build process uses xsltproc instead of sablotron
304
305
306Fixes for arb_5.1 (1 Oct 2009):
307
308 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
309 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
310 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
311 - fixed broken demo.arb
312
313
314Major changes for arb_5.00 (4 Sep 2009):
315
316 - ARB 64bit version
317 - new genome importer
318 - search for next relatives improved (normal search and fast-aligner)
319   - new parameters to precise search
320   - improved speed
321   - partial sequence reach normal scores
322 - search&query
323   - supports regular expressions and ACI
324   - track hit information
325   - result sorting
326 - Nameservers with add.field have to be started with default value
327   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
328 - multiple PT-servers may be used in parallel
329 - fixed multiprobe
330 - type-conversion for DB fields
331 - SILVA compatible import filters
332 - Newick tree export:
333   - optionally save in human-readable format (big)
334   - closer to newick standard format (quoting style, comment, special chars in data)
335 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
336 - Fixed sequence quality calculation
337 - Secondary structures for proteins (DSSP)
338 - Distance matrix (arb_dist): mark by distance to selected
339 - ARB core
340   - many bugfixes and improvements to reliability
341   - faster sorting (general speedup)
342   - improved sequence compression (avoid worse trees, better ratio)
343   - improved handling of temporary files (permission/removal)
344   - prints backtraces in userland
345   - regular expression are POSIX standard now
346 - macro record/playback
347   - fixed several bugs
348   - you need to re-record your old macros!
349 - GUI:
350   - disabled auto-focus, you need to click now
351   - auto-raise windows on access
352 - Minor things:
353   - Ubuntu: packet installation for ARB
354   - Fixed novice/expert mode
355   - Mark deep/degenerated branches
356   - Increased NDS entries
357 - up-to-date Mac port (thx to Matt Cottrell)
358
359Major changes in ARB 07.12.07org (7 Dec 2007):
360
361 - rewrote secondary structure editor
362 - Sequence quality check
363 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
364 - tweaked base frequency filter generation
365 - Normal export (not using readseq) improved:
366   - supports filters and gap removal
367   - optimized for big amount of data
368   - reworked export filters
369 - Display translation with different ORFs in EDIT4
370 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
371 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
372 - more compact display in EDIT4
373 - capable to use iso10646 fonts
374 - supports various gcc versions (2.95.3 - 4.1.1)
375 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
376 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
377   different color for size-limited circles; fixed xfig-export-bug
378 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
379 - fixed several scaling bugs in "folded tree"-mode
380 - improved import-filter error-messages
381 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
382   several new possibilities:
383   - export taxonomy via 'Export NDS list'
384   - display taxonomy in Editor etc.
385   - display of cascaded taxonomies
386   - display taxonomy of tree_1 in tree_2
387   - allows to write taxonomy into database field of species
388   - compare taxonomies of two trees
389   - ...
390 - ACI:
391   - many new ACI commands
392   - unified handling of binary ACI-operators
393   - tracing of ACI actions for debugging purpose
394 - ARB Neighbour joining:
395   - bootstrap limit configurable
396   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
397 - EDIT4:
398   - added unalign right (block-op)
399   - added 'Save loaded properties'
400 - GENE MAP:
401   - multiple views possible at the same time
402   - origin now at "12 o'clock"
403   - implemented 'jump to gene'
404 - tweaked file selection
405 - Enhanced Search Depth for Probe Match --> max 20 MM
406 - CLUSTALW:
407   - separated menus for fast and slow alignment
408   - most parameters accessible from inside ARB now
409 - upgraded to PHYLIP 3.6 (adds PROML)
410 - external programs may be called parallel (e.g. several treeing programs)
411 - fixed bugs in protml and integration of protml
412 - rewrote ASCII database import
413 - arb_repair for databases of any size (script for database repair)
414 - fixed bug in data compression
415 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
416 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
417 - GDE menus cleanup
418 - translation/re-alignment tweaked
419 - unalign right (EDIT4)
420 - visualization of SAIs in Probe Match Results
421 - changed formatting of probe match results; increase # of allowed matches to 100.000;
422   warn if results are truncated
423 - PT server for genes
424 - Probe design performance optimized
425 - fixed NEXUS export format
426 - exports group names into Newick format
427 - import XML tree files
428 - help for external tools now properly shown inside ARB
429
430Major changes in Beta 2003_08_22 (22 Aug 2003):
431
432 - automatic formatting of alignments
433 - SECEDIT may use EDIT4 colors
434 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
435 - updated clustalw to version 1.83
436 - Restore window sizes for ALL windows (too small sizes are ignored)
437 - new algorithm to add partial sequences to an existing tree
438 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
439 - Top area of ARB_NTREE may be reduced to maximize display area
440 - All arb menus may be detached (click dashed line at top of menu)
441 - visualization of SAIs (as background color behind Sequences)
442 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
443 - PT-server occupies more memory => does less passes; more diagnostic output
444 - small changes to status window (unhide behavior/time estimation)
445 - menus and menu-hotkeys reorganized
446 - colored buttons in color config windows
447 - alignment concatenation (e.g. several different genes)
448 - merging data of similar species (according selected database field)
449 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
450 - expanded sellists
451 - save/load fixed for multi probes
452 - Binary SAIs are editable in ARB_EDIT4
453 - Information windows are detachable (allows to have multiple windows showing different items)
454 - Scanning for hidden/unknown database fields improved and separated;
455   possibility to remove unused fields.
456 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
457 - updated fastDNAml to 1.2.2
458 - added AxML (accelerated fastDNAml 1.2.2)
459 - Field transfer definitions for exporting gene-species
460 - File Selection: - recursive search available
461 - The ARB_NTREE macro recording/execution has been fixed
462 - Colorize species (see demo.arb)
463 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
464 - 'IslandHopper' -- a new integrated aligner (beta)
465 - Many improvements and bugfixes to secondary structure editor:
466   - highlighting of search (i.e for probes) like in EDIT4
467   - interactive constraint editing (stretch/compress)
468   - probe info
469   - editing secondary structure in XFIG now possible
470   - visualization of SAIs
471 - import reads Unix, DOS, and MAC linefeeds
472 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
473 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
474   (reloading of these XML files is planned for the future)
475 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
476 - search in all database fields possible ('[all fields]')
477 - up to 10 quicksaves are kept
478 - new ACI functions: upper, lower, caps, eval
479 - variables for import filter programming
480 - extract gene-species: creates acc; extraction to existing alignments
481 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
482   (=> selected gene can be highlighted in primary editor)
483 - PCR primer-design for single genes
484 - when selecting a gene, the corresponding gene-species is selected (if found)
485 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
486 - file selection box in import window
487 - mark item with double click works in all search&query windows
488 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
489 - Fixed command line help for all Arb-modules
490 - Fixed problem parsing fonts (should fix display problems with default fonts)
491 - Mark mode now works in list-view as well (ARB_NTREE)
492 - Fixed appearance of 'tiny little boxes' (everywhere)
493 - Redesign of ARB help:
494     - a HTML version is in $ARBHOME/lib/help_html
495     - a text version is in $ARBHOME/lib/help (like before, but now generated)
496
497Major changes in Beta 2001_11_07 (7 Nov 2001):
498
499 - design probes to maximum length of 60 nucleotides
500 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
501 - import default changed to foreign data format, ali name '16s'
502 - printing of multi-page-trees works again
503 - implemented user defineable masks to access database fields
504 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
505 - improved performance during pt-server-build
506 - several programs coming along with ARB where updated (PHYLIP,...)
507 - reads EMBL genom files
508 - support for experiments (genom databases only)
509
510Major changes in Beta 2001_07_24 (24 Jul 2001):
511
512 - basic support for genoms (Gene Map, reads Genebank files)
513 - ported to libc6
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