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