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