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