source: tags/ms_r18q1/arb_CHANGES.txt

Last change on this file was 17110, checked in by westram, 4 years ago
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 23.5 KB
Line 
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 - DNA realigner
33   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
34     - correctly re-syncs after 'X' (if possible at all)
35     - no longer fails for 'B' and 'Z'
36     - accepts 3 or more consecutive IUPAC codes in DNA
37   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
38   * fixed several minor bugs
39 - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO)
40 - species selections (editor configurations):
41   * visualisation of multiple selections in standard tree view (#658; example in database demo.arb)
42   * order can be changed; each configuration has a comment
43 - sequence import/export:
44   * manage/edit/test import-/export-filter-definitions from inside ARB (#691)
45   * import can store configuration of imported species (#607)
46   * corrected EMBL export filter (numbers at seq.data)
47 - Tree shading (#443)
48   * according to values stored in database
49   * according to given topology (useful when comparing topologies)
50 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
51 - ARB_EDIT4:
52   * display selected database fields as flags (allowing to toggle their value; #261).
53     Example use: easily mark sequence as "curated" after manually checking its alignment.
54   * allow to load missing SAIs
55   * "view differences" to a reference sequence:
56      - customizable:
57        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
58        * case-sensitivity
59        * ignore different gap-types
60      - equal data also gets hidden in consensus
61      - refresh differences of all displayed sequences, when data of selected sequences changes
62      - change reference sequence using CTRL-R or automatically let it follow the cursor
63      - added hotkey to toggle mode: CTRL-D
64      - fixed minor bugs
65   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
66     - now both calculations are strictly consistent:
67       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
68       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
69     - added sliders to consensus definition windows
70     - user defined consensus settings exchangable between both consensus setups
71     - fixed and updated documentation
72   * added species-info mode + database save
73   * predefined SAI color translation for PVP
74 - changes to SAI generation
75   * MAX_FREQUENCY:
76     - considers IUPAC ambiguity codes proportionally
77     - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
78   * POS_VAR_BY_PARSIMONY (PVP):
79     - now (again) works with amino acid data
80 - expand zombies in tree (unfold groups)
81 - compare taxonomy (and mark differences; #651)
82 - search&query for taxonomic groups (#652)
83   - many search criteria (name, size, marked, nesting-level, ingroup-distance, ...)
84   - search multiple trees, detect duplicate and missing groups
85   - operations on found groups (delete, rename, fold, mark)
86 - added concept of "inverse groups" (aka "keeled groups")
87 - external (command line) aligners:
88   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
89   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
90   * no longer ask what to do with aligned sequence, just overwrite it
91     - only warn about real sequence changes (so please do NOT ignore from now on!)
92 - config-managers:
93   * possibility to restore factory defaults
94   * added comment field for configurations
95   * added them throughout arb (#647)
96 - added slide controls throughout arb (#656)
97 - tree (display) options:
98   * fine grained scaling
99   * add threshold for visible support values
100   * group display (shading, customizable counters, triangle clades, optimized name+bootstrap display position)
101   * diagonal branch style
102   * parent branch position
103   * all options are now also supported by ARB_PARSIMONY
104   * improved auto-jump; now also works for groups
105   * added optional auto-unfolding (to selected group/species)
106   * select group on fold/unfold/create/move/..
107   * draw selected group in cursor-color
108   * added keys for tree-traversal (moving selected species or group)
109 - synchronized tree scrolling (#683)
110 - colorsets were invalidated by generating new IDs (#660). fixed.
111 - added alternate RAxML (DNA only; version 8.2.8)
112   - multicore support (automatically activates recommended number of threads)
113   - evaluation, optimization and extension of existing trees with RAxML
114 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
115 - ACI
116   - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands
117   - improved ACI debugging: more verbose tracing (console log accessible from inside ARB)
118 - NDS optionally uses only visible definitions
119 - Search&Query (sort results numerically, improved macro compatibility)
120 - Species info (improved detachment, field selection + macro compatibility)
121 - updated integrated documentation
122
123Fixes for arb-6.0.5 (4 May 2016):
124
125 - fixes for ubuntu 16.04 build
126
127Fixes for arb-6.0.4 (2 May 2016):
128
129 - fixes for OSX build (SIP, accepted compilers)
130
131Fixes for arb-6.0.3 (19 Nov 2015):
132
133 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
134
135Fixes for arb-6.0.2 (8 Aug 2014):
136
137 - compile issues on Snow Leopard (OSX 10.6)
138 - merge Debian security fix for CVE-2008-5378
139 - small changes to build system for Debian
140 - add desktop integration files
141
142Fixes for arb-6.0.1 (22 Jul 2014):
143
144 - arb_parsimony
145   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
146   - corrected branchlength calculation for "Add marked partial species"
147   - 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!
148 - print
149   - preview failed (showed empty postscript file)
150   - print to file now always saves in user home
151 - raxml (import tree with bootstrap values)
152
153Major changes for arb-6.0 (4 Jun 2014):
154
155 - merge databases allows to
156   - merge from an existing database into the database loaded in ARB_NT
157   - merge to existing databases from the database loaded in ARB_NT
158 - ARB can now
159   - be restarted with another database and
160   - a second instance of ARB can be opened
161 - ARB_DIST
162   - Detect clusters of species with similar sequences (OTUs)
163   - allow automatic recalculation of matrix and/or tree whenever some parameter or
164     data changes (only makes sense for smaller species sets)
165   - extract distance matrix from tree
166 - Rewrote chimera check. Allows filtering
167 - added RNACMA (computes clusters of correlated positions)
168 - PT-Server
169   - changed behavior
170     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
171     - reports previously missing hits in joined genes
172     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
173       matches that go beyond the end of the sequence)
174     - dots in the middle of the alignment act like the sequence ends there
175     - minimum probe length reduced to 2 (was 6)
176     - allow up to 50% of probe to mismatch
177   - performance
178     - optimized memory-estimation (will build in fewer passes)
179     - uses any number of passes (not only 1, 5, 25, ...)
180     - allows to define used memory by setting environment variable ARB_MEMORY
181     - reduced memory needed to build/run ptserver (approx. 50%)
182     - reduced size of indexfile (.pt) to ~50%
183     - fast startup of existing ptservers
184   - probe design
185     - faster in many cases
186     - allow to design probes of length 8 (previously 10)
187     - allow to design probes with different lengths (specifying min/max length)
188     - fixed number of outgroup hits reported when decreasing temperature
189       (now each outgroup member only occurs once)
190     - show possible reasons why no probes could be designed
191   - probe match (allow any number of mismatches)
192   - next relative search
193     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
194     - corrected and improved scaling of relative scores
195     - more accurate scores (due to fixes in PT-Server; see below)
196     - faster in many cases
197   - show errors from ptserver build in ARB
198 - fast-aligner
199   - searches next-relatives based on selected column-block
200   - align multiple column-blocks based on SAI
201 - Rewrote alignment adaption during merge
202 - Insert/delete columns using a SAI to define affected columns
203 - ARB_EDIT4
204   - improved support for using multiple edit-windows
205   - smoother refreshes
206   - tweaked ORF display
207 - tree importer/exporter
208   - ARBs extended newick format (with bootstrap values) handled more restrictive now
209   - fixed several bugs; improved errors/warnings
210 - consensus trees
211   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
212   - fixed NJ-bootstrapping (no longer drops species)
213 - tree display
214   - Show brackets on open groups (dendrogram tree only)
215   - rewrote IRS (folded) display
216   - fixed tree key-bindings (mark, fold, ...)
217   - improved several tree-commands (move, rotate, spread, length, width)
218 - added a branch analysis tool
219   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
220   - added leaf-distance analysis
221 - other tree functionality
222   - treelist sortable now
223   - new beautify-tree modes (radial tree / according to other tree)
224   - function to remove marked/zombies from ALL trees
225   - create multifurcations (by branchlength/bootstrap limit)
226   - toggle 100% bootstrap values
227 - tweaked printing (interface, overlapping)
228 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
229 - probe design:
230   - added LOAD to result window
231 - automation
232   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
233   - arb_ntree can execute macro from command line
234   - added "Never ask again" to modal question boxes (for better compatibility with macros)
235   - a macro can be called for all marked species (once for each)
236   - macros can be nested (i.e. can call other macros)
237 - support for user-specific customization:
238   - of GDE menus (in ~/.arb_prop/gde)
239   - of import/export filters (in ~/.arb_prop/filter)
240 - ACI (some new commands, bugfixes)
241 - updated/added external tools:
242   - added FastTree (version 2.1.7)
243   - added MAFFT (version 7.055)
244   - added MrBayes (version 3.2.1)
245   - added MUSCLE (version 3.8.31)
246   - added PHYML (2013/07/08; also kept old version 2.4.5)
247   - added PROBCONS (version 1.12)
248   - updated RAxML (version 7.7.2)
249 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
250 - Support for mouse-wheel
251 - many unlisted bugfixes
252 - many internal refactorings
253
254
255Fixes for arb_5.5 (15 Nov 2012):
256
257 * arb_5.4 was broken (several external tools missing)
258
259
260Fixes for arb_5.4 (14 Nov 2012):
261
262 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
263 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
264 * fixed several compilation issues (OSX; recent distro releases)
265
266
267Fixes for arb_5.3 (10 Nov 2011):
268
269 - bugfixes
270   - fixed wrong absolute/ecoli position reported for some designed probes
271   - decompression error handling (pt-server build issues)
272   - fixed 'codon_start' generated with wrong type
273   - fixed a buffer overflow in ACI
274   - report failures to write to /tmp
275 - changes
276   - markSpecies.pl:
277     mark by accession number
278     partial/ambiguous matches
279 - internal fixes
280   - compilation fixes for OSX
281   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
282   - removed obsolete dependency from libXp
283
284
285Fixes for arb_5.2 (5 Sep 2010):
286
287 - bugfixes
288   - quicksave did silently do nothing (especially not save anything) if an error occurred
289   - ARB_EDIT4: crashed when using config with MANY unknown species
290   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
291   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
292 - changes
293   - ARB uses xdg-open to display web-pages
294 - internal fixes
295   - karmic koala (gcc 4.4.1)
296   - installation script
297   - arb build process uses xsltproc instead of sablotron
298
299
300Fixes for arb_5.1 (1 Oct 2009):
301
302 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
303 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
304 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
305 - fixed broken demo.arb
306
307
308Major changes for arb_5.00 (4 Sep 2009):
309
310 - ARB 64bit version
311 - new genome importer
312 - search for next relatives improved (normal search and fast-aligner)
313   - new parameters to precise search
314   - improved speed
315   - partial sequence reach normal scores
316 - search&query
317   - supports regular expressions and ACI
318   - track hit information
319   - result sorting
320 - Nameservers with add.field have to be started with default value
321   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
322 - multiple PT-servers may be used in parallel
323 - fixed multiprobe
324 - type-conversion for DB fields
325 - SILVA compatible import filters
326 - Newick tree export:
327   - optionally save in human-readable format (big)
328   - closer to newick standard format (quoting style, comment, special chars in data)
329 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
330 - Fixed sequence quality calculation
331 - Secondary structures for proteins (DSSP)
332 - Distance matrix (arb_dist): mark by distance to selected
333 - ARB core
334   - many bugfixes and improvements to reliability
335   - faster sorting (general speedup)
336   - improved sequence compression (avoid worse trees, better ratio)
337   - improved handling of temporary files (permission/removal)
338   - prints backtraces in userland
339   - regular expression are POSIX standard now
340 - macro record/playback
341   - fixed several bugs
342   - you need to re-record your old macros!
343 - GUI:
344   - disabled auto-focus, you need to click now
345   - auto-raise windows on access
346 - Minor things:
347   - Ubuntu: packet installation for ARB
348   - Fixed novice/expert mode
349   - Mark deep/degenerated branches
350   - Increased NDS entries
351 - up-to-date Mac port (thx to Matt Cottrell)
352
353Major changes in ARB 07.12.07org (7 Dec 2007):
354
355 - rewrote secondary structure editor
356 - Sequence quality check
357 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
358 - tweaked base frequency filter generation
359 - Normal export (not using readseq) improved:
360   - supports filters and gap removal
361   - optimized for big amount of data
362   - reworked export filters
363 - Display translation with different ORFs in EDIT4
364 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
365 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
366 - more compact display in EDIT4
367 - capable to use iso10646 fonts
368 - supports various gcc versions (2.95.3 - 4.1.1)
369 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
370 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
371   different color for size-limited circles; fixed xfig-export-bug
372 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
373 - fixed several scaling bugs in "folded tree"-mode
374 - improved import-filter error-messages
375 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
376   several new possibilities:
377   - export taxonomy via 'Export NDS list'
378   - display taxonomy in Editor etc.
379   - display of cascaded taxonomies
380   - display taxonomy of tree_1 in tree_2
381   - allows to write taxonomy into database field of species
382   - compare taxonomies of two trees
383   - ...
384 - ACI:
385   - many new ACI commands
386   - unified handling of binary ACI-operators
387   - tracing of ACI actions for debugging purpose
388 - ARB Neighbour joining:
389   - bootstrap limit configurable
390   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
391 - EDIT4:
392   - added unalign right (block-op)
393   - added 'Save loaded properties'
394 - GENE MAP:
395   - multiple views possible at the same time
396   - origin now at "12 o'clock"
397   - implemented 'jump to gene'
398 - tweaked file selection
399 - Enhanced Search Depth for Probe Match --> max 20 MM
400 - CLUSTALW:
401   - separated menus for fast and slow alignment
402   - most parameters accessible from inside ARB now
403 - upgraded to PHYLIP 3.6 (adds PROML)
404 - external programs may be called parallel (e.g. several treeing programs)
405 - fixed bugs in protml and integration of protml
406 - rewrote ASCII database import
407 - arb_repair for databases of any size (script for database repair)
408 - fixed bug in data compression
409 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
410 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
411 - GDE menus cleanup
412 - translation/re-alignment tweaked
413 - unalign right (EDIT4)
414 - visualization of SAIs in Probe Match Results
415 - changed formatting of probe match results; increase # of allowed matches to 100.000;
416   warn if results are truncated
417 - PT server for genes
418 - Probe design performance optimized
419 - fixed NEXUS export format
420 - exports group names into Newick format
421 - import XML tree files
422 - help for external tools now properly shown inside ARB
423
424Major changes in Beta 2003_08_22 (22 Aug 2003):
425
426 - automatic formatting of alignments
427 - SECEDIT may use EDIT4 colors
428 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
429 - updated clustalw to version 1.83
430 - Restore window sizes for ALL windows (too small sizes are ignored)
431 - new algorithm to add partial sequences to an existing tree
432 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
433 - Top area of ARB_NTREE may be reduced to maximize display area
434 - All arb menus may be detached (click dashed line at top of menu)
435 - visualization of SAIs (as background color behind Sequences)
436 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
437 - PT-server occupies more memory => does less passes; more diagnostic output
438 - small changes to status window (unhide behavior/time estimation)
439 - menus and menu-hotkeys reorganized
440 - colored buttons in color config windows
441 - alignment concatenation (e.g. several different genes)
442 - merging data of similar species (according selected database field)
443 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
444 - expanded sellists
445 - save/load fixed for multi probes
446 - Binary SAIs are editable in ARB_EDIT4
447 - Information windows are detachable (allows to have multiple windows showing different items)
448 - Scanning for hidden/unknown database fields improved and separated;
449   possibility to remove unused fields.
450 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
451 - updated fastDNAml to 1.2.2
452 - added AxML (accelerated fastDNAml 1.2.2)
453 - Field transfer definitions for exporting gene-species
454 - File Selection: - recursive search available
455 - The ARB_NTREE macro recording/execution has been fixed
456 - Colorize species (see demo.arb)
457 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
458 - 'IslandHopper' -- a new integrated aligner (beta)
459 - Many improvements and bugfixes to secondary structure editor:
460   - highlighting of search (i.e for probes) like in EDIT4
461   - interactive constraint editing (stretch/compress)
462   - probe info
463   - editing secondary structure in XFIG now possible
464   - visualization of SAIs
465 - import reads Unix, DOS, and MAC linefeeds
466 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
467 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
468   (reloading of these XML files is planned for the future)
469 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
470 - search in all database fields possible ('[all fields]')
471 - up to 10 quicksaves are kept
472 - new ACI functions: upper, lower, caps, eval
473 - variables for import filter programming
474 - extract gene-species: creates acc; extraction to existing alignments
475 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
476   (=> selected gene can be highlighted in primary editor)
477 - PCR primer-design for single genes
478 - when selecting a gene, the corresponding gene-species is selected (if found)
479 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
480 - file selection box in import window
481 - mark item with double click works in all search&query windows
482 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
483 - Fixed command line help for all Arb-modules
484 - Fixed problem parsing fonts (should fix display problems with default fonts)
485 - Mark mode now works in list-view as well (ARB_NTREE)
486 - Fixed appearance of 'tiny little boxes' (everywhere)
487 - Redesign of ARB help:
488     - a HTML version is in $ARBHOME/lib/help_html
489     - a text version is in $ARBHOME/lib/help (like before, but now generated)
490
491Major changes in Beta 2001_11_07 (7 Nov 2001):
492
493 - design probes to maximum length of 60 nucleotides
494 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
495 - import default changed to foreign data format, ali name '16s'
496 - printing of multi-page-trees works again
497 - implemented user defineable masks to access database fields
498 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
499 - improved performance during pt-server-build
500 - several programs coming along with ARB where updated (PHYLIP,...)
501 - reads EMBL genom files
502 - support for experiments (genom databases only)
503
504Major changes in Beta 2001_07_24 (24 Jul 2001):
505
506 - basic support for genoms (Gene Map, reads Genebank files)
507 - ported to libc6
Note: See TracBrowser for help on using the repository browser.