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