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 - import/export (species,sequence):
46   * manage/edit/test import-/export-filter-definitions from inside ARB (#691)
47   * import can store configuration of imported species (#607)
48   * field transfer sets (#562) may be used to customize import/export behavior (also usable from arb merge-tool)
49   * corrected EMBL export filter (numbers at seq.data)
50 - Tree shading (#443)
51   * according to values stored in database
52   * according to given topology (useful when comparing topologies)
53 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
54 - ARB_EDIT4:
55   * display selected database fields as flags (allowing to toggle their value; #261).
56     Example use: easily mark sequence as "curated" after manually checking its alignment.
57   * allow to load missing SAIs
58   * "view differences" to a reference sequence:
59      - customizable:
60        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
61        * case-sensitivity
62        * ignore different gap-types
63      - equal data also gets hidden in consensus
64      - refresh differences of all displayed sequences, when data of selected sequences changes
65      - change reference sequence using CTRL-R or automatically let it follow the cursor
66      - added hotkey to toggle mode: CTRL-D
67      - fixed minor bugs
68   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
69     - now both calculations are strictly consistent:
70       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
71       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
72     - added sliders to consensus definition windows
73     - user defined consensus settings exchangable between both consensus setups
74     - fixed and updated documentation
75   * added species-info mode + database save
76   * predefined SAI color translation for PVP
77 - changes to SAI generation
78   * MAX_FREQUENCY:
79     - considers IUPAC ambiguity codes proportionally
80     - amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
81   * POS_VAR_BY_PARSIMONY (PVP):
82     - now (again) works with amino acid data
83 - expand zombies in tree (unfold groups)
84 - compare taxonomy (and mark differences; #651)
85 - search&query for taxonomic groups (#652)
86   - many search criteria (name, size, marked, nesting-level, ingroup-distance, ...)
87   - search multiple trees, detect duplicate and missing groups
88   - operations on found groups (delete, rename, fold, mark)
89 - added concept of "inverse groups" (aka "keeled groups")
90 - group transfer between trees:
91   - penalties can be customized in detail
92   - quality reports (to log and optionally to target name)
93 - external (command line) aligners:
94   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
95   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
96   * no longer ask what to do with aligned sequence, just overwrite it
97     - only warn about real sequence changes (so please do NOT ignore from now on!)
98 - config-managers:
99   * possibility to restore factory defaults
100   * added comment field for configurations
101   * added them throughout arb (#647)
102 - added slide controls throughout arb (#656)
103 - tree (display) options:
104   * fine grained scaling
105   * add threshold for visible support values
106   * group display (shading, customizable counters, triangle clades, name display position)
107   * bootstrap values (filter by upper/lower limits, display position/styles, on/off toggle)
108   * diagonal branch style
109   * parent branch position
110   * all options are now also supported by ARB_PARSIMONY
111   * improved auto-jump; now also works for groups
112   * added optional auto-unfolding (to selected group/species)
113   * select group on fold/unfold/create/move/..
114   * draw selected group in cursor-color
115   * added keys for tree-traversal (moving selected species or group)
116 - synchronized tree scrolling (#683)
117 - colorsets were invalidated by generating new IDs (#660). fixed.
118 - added alternate RAxML (DNA only; version 8.2.8)
119   - multicore support (automatically activates recommended number of threads)
120   - evaluation, optimization and extension of existing trees with RAxML
121 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
122 - ACI
123   - added boolean operators, numeric comparisons, floating point arithmetic and several other new commands
124   - improved ACI debugging: more verbose tracing (console log accessible from inside ARB)
125 - NDS optionally uses only visible definitions
126 - Search&Query (sort results numerically, improved macro compatibility)
127 - Species info (improved detachment, field selection + macro compatibility)
128 - updated integrated documentation
129
130Fixes for arb-6.0.5 (4 May 2016):
131
132 - fixes for ubuntu 16.04 build
133
134Fixes for arb-6.0.4 (2 May 2016):
135
136 - fixes for OSX build (SIP, accepted compilers)
137
138Fixes for arb-6.0.3 (19 Nov 2015):
139
140 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
141
142Fixes for arb-6.0.2 (8 Aug 2014):
143
144 - compile issues on Snow Leopard (OSX 10.6)
145 - merge Debian security fix for CVE-2008-5378
146 - small changes to build system for Debian
147 - add desktop integration files
148
149Fixes for arb-6.0.1 (22 Jul 2014):
150
151 - arb_parsimony
152   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
153   - corrected branchlength calculation for "Add marked partial species"
154   - 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!
155 - print
156   - preview failed (showed empty postscript file)
157   - print to file now always saves in user home
158 - raxml (import tree with bootstrap values)
159
160Major changes for arb-6.0 (4 Jun 2014):
161
162 - merge databases allows to
163   - merge from an existing database into the database loaded in ARB_NT
164   - merge to existing databases from the database loaded in ARB_NT
165 - ARB can now
166   - be restarted with another database and
167   - a second instance of ARB can be opened
168 - ARB_DIST
169   - Detect clusters of species with similar sequences (OTUs)
170   - allow automatic recalculation of matrix and/or tree whenever some parameter or
171     data changes (only makes sense for smaller species sets)
172   - extract distance matrix from tree
173 - Rewrote chimera check. Allows filtering
174 - added RNACMA (computes clusters of correlated positions)
175 - PT-Server
176   - changed behavior
177     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
178     - reports previously missing hits in joined genes
179     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
180       matches that go beyond the end of the sequence)
181     - dots in the middle of the alignment act like the sequence ends there
182     - minimum probe length reduced to 2 (was 6)
183     - allow up to 50% of probe to mismatch
184   - performance
185     - optimized memory-estimation (will build in fewer passes)
186     - uses any number of passes (not only 1, 5, 25, ...)
187     - allows to define used memory by setting environment variable ARB_MEMORY
188     - reduced memory needed to build/run ptserver (approx. 50%)
189     - reduced size of indexfile (.pt) to ~50%
190     - fast startup of existing ptservers
191   - probe design
192     - faster in many cases
193     - allow to design probes of length 8 (previously 10)
194     - allow to design probes with different lengths (specifying min/max length)
195     - fixed number of outgroup hits reported when decreasing temperature
196       (now each outgroup member only occurs once)
197     - show possible reasons why no probes could be designed
198   - probe match (allow any number of mismatches)
199   - next relative search
200     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
201     - corrected and improved scaling of relative scores
202     - more accurate scores (due to fixes in PT-Server; see below)
203     - faster in many cases
204   - show errors from ptserver build in ARB
205 - fast-aligner
206   - searches next-relatives based on selected column-block
207   - align multiple column-blocks based on SAI
208 - Rewrote alignment adaption during merge
209 - Insert/delete columns using a SAI to define affected columns
210 - ARB_EDIT4
211   - improved support for using multiple edit-windows
212   - smoother refreshes
213   - tweaked ORF display
214 - tree importer/exporter
215   - ARBs extended newick format (with bootstrap values) handled more restrictive now
216   - fixed several bugs; improved errors/warnings
217 - consensus trees
218   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
219   - fixed NJ-bootstrapping (no longer drops species)
220 - tree display
221   - Show brackets on open groups (dendrogram tree only)
222   - rewrote IRS (folded) display
223   - fixed tree key-bindings (mark, fold, ...)
224   - improved several tree-commands (move, rotate, spread, length, width)
225 - added a branch analysis tool
226   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
227   - added leaf-distance analysis
228 - other tree functionality
229   - treelist sortable now
230   - new beautify-tree modes (radial tree / according to other tree)
231   - function to remove marked/zombies from ALL trees
232   - create multifurcations (by branchlength/bootstrap limit)
233   - toggle 100% bootstrap values
234 - tweaked printing (interface, overlapping)
235 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
236 - probe design:
237   - added LOAD to result window
238 - automation
239   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
240   - arb_ntree can execute macro from command line
241   - added "Never ask again" to modal question boxes (for better compatibility with macros)
242   - a macro can be called for all marked species (once for each)
243   - macros can be nested (i.e. can call other macros)
244 - support for user-specific customization:
245   - of GDE menus (in ~/.arb_prop/gde)
246   - of import/export filters (in ~/.arb_prop/filter)
247 - ACI (some new commands, bugfixes)
248 - updated/added external tools:
249   - added FastTree (version 2.1.7)
250   - added MAFFT (version 7.055)
251   - added MrBayes (version 3.2.1)
252   - added MUSCLE (version 3.8.31)
253   - added PHYML (2013/07/08; also kept old version 2.4.5)
254   - added PROBCONS (version 1.12)
255   - updated RAxML (version 7.7.2)
256 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
257 - Support for mouse-wheel
258 - many unlisted bugfixes
259 - many internal refactorings
260
261
262Fixes for arb_5.5 (15 Nov 2012):
263
264 * arb_5.4 was broken (several external tools missing)
265
266
267Fixes for arb_5.4 (14 Nov 2012):
268
269 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
270 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
271 * fixed several compilation issues (OSX; recent distro releases)
272
273
274Fixes for arb_5.3 (10 Nov 2011):
275
276 - bugfixes
277   - fixed wrong absolute/ecoli position reported for some designed probes
278   - decompression error handling (pt-server build issues)
279   - fixed 'codon_start' generated with wrong type
280   - fixed a buffer overflow in ACI
281   - report failures to write to /tmp
282 - changes
283   - markSpecies.pl:
284     mark by accession number
285     partial/ambiguous matches
286 - internal fixes
287   - compilation fixes for OSX
288   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
289   - removed obsolete dependency from libXp
290
291
292Fixes for arb_5.2 (5 Sep 2010):
293
294 - bugfixes
295   - quicksave did silently do nothing (especially not save anything) if an error occurred
296   - ARB_EDIT4: crashed when using config with MANY unknown species
297   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
298   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
299 - changes
300   - ARB uses xdg-open to display web-pages
301 - internal fixes
302   - karmic koala (gcc 4.4.1)
303   - installation script
304   - arb build process uses xsltproc instead of sablotron
305
306
307Fixes for arb_5.1 (1 Oct 2009):
308
309 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
310 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
311 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
312 - fixed broken demo.arb
313
314
315Major changes for arb_5.00 (4 Sep 2009):
316
317 - ARB 64bit version
318 - new genome importer
319 - search for next relatives improved (normal search and fast-aligner)
320   - new parameters to precise search
321   - improved speed
322   - partial sequence reach normal scores
323 - search&query
324   - supports regular expressions and ACI
325   - track hit information
326   - result sorting
327 - Nameservers with add.field have to be started with default value
328   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
329 - multiple PT-servers may be used in parallel
330 - fixed multiprobe
331 - type-conversion for DB fields
332 - SILVA compatible import filters
333 - Newick tree export:
334   - optionally save in human-readable format (big)
335   - closer to newick standard format (quoting style, comment, special chars in data)
336 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
337 - Fixed sequence quality calculation
338 - Secondary structures for proteins (DSSP)
339 - Distance matrix (arb_dist): mark by distance to selected
340 - ARB core
341   - many bugfixes and improvements to reliability
342   - faster sorting (general speedup)
343   - improved sequence compression (avoid worse trees, better ratio)
344   - improved handling of temporary files (permission/removal)
345   - prints backtraces in userland
346   - regular expression are POSIX standard now
347 - macro record/playback
348   - fixed several bugs
349   - you need to re-record your old macros!
350 - GUI:
351   - disabled auto-focus, you need to click now
352   - auto-raise windows on access
353 - Minor things:
354   - Ubuntu: packet installation for ARB
355   - Fixed novice/expert mode
356   - Mark deep/degenerated branches
357   - Increased NDS entries
358 - up-to-date Mac port (thx to Matt Cottrell)
359
360Major changes in ARB 07.12.07org (7 Dec 2007):
361
362 - rewrote secondary structure editor
363 - Sequence quality check
364 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
365 - tweaked base frequency filter generation
366 - Normal export (not using readseq) improved:
367   - supports filters and gap removal
368   - optimized for big amount of data
369   - reworked export filters
370 - Display translation with different ORFs in EDIT4
371 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
372 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
373 - more compact display in EDIT4
374 - capable to use iso10646 fonts
375 - supports various gcc versions (2.95.3 - 4.1.1)
376 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
377 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
378   different color for size-limited circles; fixed xfig-export-bug
379 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
380 - fixed several scaling bugs in "folded tree"-mode
381 - improved import-filter error-messages
382 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
383   several new possibilities:
384   - export taxonomy via 'Export NDS list'
385   - display taxonomy in Editor etc.
386   - display of cascaded taxonomies
387   - display taxonomy of tree_1 in tree_2
388   - allows to write taxonomy into database field of species
389   - compare taxonomies of two trees
390   - ...
391 - ACI:
392   - many new ACI commands
393   - unified handling of binary ACI-operators
394   - tracing of ACI actions for debugging purpose
395 - ARB Neighbour joining:
396   - bootstrap limit configurable
397   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
398 - EDIT4:
399   - added unalign right (block-op)
400   - added 'Save loaded properties'
401 - GENE MAP:
402   - multiple views possible at the same time
403   - origin now at "12 o'clock"
404   - implemented 'jump to gene'
405 - tweaked file selection
406 - Enhanced Search Depth for Probe Match --> max 20 MM
407 - CLUSTALW:
408   - separated menus for fast and slow alignment
409   - most parameters accessible from inside ARB now
410 - upgraded to PHYLIP 3.6 (adds PROML)
411 - external programs may be called parallel (e.g. several treeing programs)
412 - fixed bugs in protml and integration of protml
413 - rewrote ASCII database import
414 - arb_repair for databases of any size (script for database repair)
415 - fixed bug in data compression
416 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
417 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
418 - GDE menus cleanup
419 - translation/re-alignment tweaked
420 - unalign right (EDIT4)
421 - visualization of SAIs in Probe Match Results
422 - changed formatting of probe match results; increase # of allowed matches to 100.000;
423   warn if results are truncated
424 - PT server for genes
425 - Probe design performance optimized
426 - fixed NEXUS export format
427 - exports group names into Newick format
428 - import XML tree files
429 - help for external tools now properly shown inside ARB
430
431Major changes in Beta 2003_08_22 (22 Aug 2003):
432
433 - automatic formatting of alignments
434 - SECEDIT may use EDIT4 colors
435 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
436 - updated clustalw to version 1.83
437 - Restore window sizes for ALL windows (too small sizes are ignored)
438 - new algorithm to add partial sequences to an existing tree
439 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
440 - Top area of ARB_NTREE may be reduced to maximize display area
441 - All arb menus may be detached (click dashed line at top of menu)
442 - visualization of SAIs (as background color behind Sequences)
443 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
444 - PT-server occupies more memory => does less passes; more diagnostic output
445 - small changes to status window (unhide behavior/time estimation)
446 - menus and menu-hotkeys reorganized
447 - colored buttons in color config windows
448 - alignment concatenation (e.g. several different genes)
449 - merging data of similar species (according selected database field)
450 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
451 - expanded sellists
452 - save/load fixed for multi probes
453 - Binary SAIs are editable in ARB_EDIT4
454 - Information windows are detachable (allows to have multiple windows showing different items)
455 - Scanning for hidden/unknown database fields improved and separated;
456   possibility to remove unused fields.
457 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
458 - updated fastDNAml to 1.2.2
459 - added AxML (accelerated fastDNAml 1.2.2)
460 - Field transfer definitions for exporting gene-species
461 - File Selection: - recursive search available
462 - The ARB_NTREE macro recording/execution has been fixed
463 - Colorize species (see demo.arb)
464 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
465 - 'IslandHopper' -- a new integrated aligner (beta)
466 - Many improvements and bugfixes to secondary structure editor:
467   - highlighting of search (i.e for probes) like in EDIT4
468   - interactive constraint editing (stretch/compress)
469   - probe info
470   - editing secondary structure in XFIG now possible
471   - visualization of SAIs
472 - import reads Unix, DOS, and MAC linefeeds
473 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
474 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
475   (reloading of these XML files is planned for the future)
476 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
477 - search in all database fields possible ('[all fields]')
478 - up to 10 quicksaves are kept
479 - new ACI functions: upper, lower, caps, eval
480 - variables for import filter programming
481 - extract gene-species: creates acc; extraction to existing alignments
482 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
483   (=> selected gene can be highlighted in primary editor)
484 - PCR primer-design for single genes
485 - when selecting a gene, the corresponding gene-species is selected (if found)
486 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
487 - file selection box in import window
488 - mark item with double click works in all search&query windows
489 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
490 - Fixed command line help for all Arb-modules
491 - Fixed problem parsing fonts (should fix display problems with default fonts)
492 - Mark mode now works in list-view as well (ARB_NTREE)
493 - Fixed appearance of 'tiny little boxes' (everywhere)
494 - Redesign of ARB help:
495     - a HTML version is in $ARBHOME/lib/help_html
496     - a text version is in $ARBHOME/lib/help (like before, but now generated)
497
498Major changes in Beta 2001_11_07 (7 Nov 2001):
499
500 - design probes to maximum length of 60 nucleotides
501 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
502 - import default changed to foreign data format, ali name '16s'
503 - printing of multi-page-trees works again
504 - implemented user defineable masks to access database fields
505 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
506 - improved performance during pt-server-build
507 - several programs coming along with ARB where updated (PHYLIP,...)
508 - reads EMBL genom files
509 - support for experiments (genom databases only)
510
511Major changes in Beta 2001_07_24 (24 Jul 2001):
512
513 - basic support for genoms (Gene Map, reads Genebank files)
514 - ported to libc6
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