source: tags/ms_r16q2/arb_CHANGES.txt

Last change on this file was 14841, checked in by westram, 6 years ago
  • fixes #702 by lazy-loading sequence data
  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
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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   * generally reduced the number of performed combines (skipping many useless)
23   * added function to randomize (parts of) the tree
24   * warns about insufficient sequence data (e.g. as result of too restrictive filtering; #631)
25   * fixed 'RESTORE' (crashed after deleting species from tree; #528)
26   * corrected handling of dots ('.') while combining anchestor sequences
27   * fixed a bunch of internal bugs (#620, #627, ...)
28   * added species-info
29 - DNA realigner
30   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
31     - correctly re-syncs after 'X' (if possible at all)
32     - no longer fails for 'B' and 'Z'
33     - accepts 3 or more consecutive IUPAC codes in DNA
34   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
35   * fixed several minor bugs
36 - ARB probeSpec: visualisation of probe set specificity (thanks to Paavo Jumppanen, CSIRO)
37 - species selections (editor configurations):
38   * visualisation of multiple selections in standard tree view (#658; example in database demo.arb)
39   * order can be changed; each configuration has a comment; import stores configuration (#607)
40 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
41 - ARB_EDIT4:
42   * allow to load missing SAIs
43   * "view differences" to a reference sequence:
44      - customizable:
45        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
46        * case-sensitivity
47        * ignore different gap-types
48      - equal data also gets hidden in consensus
49      - refresh differences of all displayed sequences, when data of selected sequences changes
50      - change reference sequence using CTRL-R or automatically let it follow the cursor
51      - added hotkey to toggle mode: CTRL-D
52      - fixed minor bugs
53   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
54     - now both calculations are strictly consistent:
55       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
56       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
57     - added sliders to consensus definition windows
58     - user defined consensus settings exchangable between both consensus setups
59     - fixed and updated documentation
60   * added species-info + database save
61 - SAI: MAX_FREQUENCY
62   * considers IUPAC ambiguity codes proportionally
63   * amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
64 - expand zombies in tree (unfold groups)
65 - compare taxonomy (and mark differences; #651)
66 - external (command line) aligners:
67   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
68   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
69   * no longer ask what to do with aligned sequence, just overwrite it
70     - only warn about real sequence changes (so please do NOT ignore from now on!)
71 - config-managers:
72   * possibility to restore factory defaults
73   * added comment field for configurations
74   * added them throughout arb (#647)
75 - added slide controls throughout arb (#656)
76 - tree (display) options:
77   * fine grained scaling
78   * improved auto-jump
79   * add threshold for visible support values
80   * group shading
81   * group counters (customizable)
82   * all options are now also supported by ARB_PARSIMONY
83 - colorsets were invalidated by generating new IDs (#660). fixed.
84 - updated/added external tools:
85   - added alternate RAxML (DNA only; version 8.0.26)
86 - updated integrated documentation
87 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
88
89Minor changes
90 - corrected EMBL export filter (numbers at seq.data)
91 - NDS optionally uses only visible definitions
92
93Fixes for arb-6.0.5 (4 May 2016):
94
95 - fixes for ubuntu 16.04 build
96
97Fixes for arb-6.0.4 (2 May 2016):
98
99 - fixes for OSX build (SIP, accepted compilers)
100
101Fixes for arb-6.0.3 (19 Nov 2015):
102
103 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
104
105Fixes for arb-6.0.2 (8 Aug 2014):
106
107 - compile issues on Snow Leopard (OSX 10.6)
108 - merge Debian security fix for CVE-2008-5378
109 - small changes to build system for Debian
110 - add desktop integration files
111
112Fixes for arb-6.0.1 (22 Jul 2014):
113
114 - arb_parsimony
115   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
116   - corrected branchlength calculation for "Add marked partial species"
117   - 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!
118 - print
119   - preview failed (showed empty postscript file)
120   - print to file now always saves in user home
121 - raxml (import tree with bootstrap values)
122
123Major changes for arb-6.0 (4 Jun 2014):
124
125 - merge databases allows to
126   - merge from an existing database into the database loaded in ARB_NT
127   - merge to existing databases from the database loaded in ARB_NT
128 - ARB can now
129   - be restarted with another database and
130   - a second instance of ARB can be opened
131 - ARB_DIST
132   - Detect clusters of species with similar sequences (OTUs)
133   - allow automatic recalculation of matrix and/or tree whenever some parameter or
134     data changes (only makes sense for smaller species sets)
135   - extract distance matrix from tree
136 - Rewrote chimera check. Allows filtering
137 - added RNACMA (computes clusters of correlated positions)
138 - PT-Server
139   - changed behavior
140     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
141     - reports previously missing hits in joined genes
142     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
143       matches that go beyond the end of the sequence)
144     - dots in the middle of the alignment act like the sequence ends there
145     - minimum probe length reduced to 2 (was 6)
146     - allow up to 50% of probe to mismatch
147   - performance
148     - optimized memory-estimation (will build in fewer passes)
149     - uses any number of passes (not only 1, 5, 25, ...)
150     - allows to define used memory by setting environment variable ARB_MEMORY
151     - reduced memory needed to build/run ptserver (approx. 50%)
152     - reduced size of indexfile (.pt) to ~50%
153     - fast startup of existing ptservers
154   - probe design
155     - faster in many cases
156     - allow to design probes of length 8 (previously 10)
157     - allow to design probes with different lengths (specifying min/max length)
158     - fixed number of outgroup hits reported when decreasing temperature
159       (now each outgroup member only occurs once)
160     - show possible reasons why no probes could be designed
161   - probe match (allow any number of mismatches)
162   - next relative search
163     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
164     - corrected and improved scaling of relative scores
165     - more accurate scores (due to fixes in PT-Server; see below)
166     - faster in many cases
167   - show errors from ptserver build in ARB
168 - fast-aligner
169   - searches next-relatives based on selected column-block
170   - align multiple column-blocks based on SAI
171 - Rewrote alignment adaption during merge
172 - Insert/delete columns using a SAI to define affected columns
173 - ARB_EDIT4
174   - improved support for using multiple edit-windows
175   - smoother refreshes
176   - tweaked ORF display
177 - tree importer/exporter
178   - ARBs extended newick format (with bootstrap values) handled more restrictive now
179   - fixed several bugs; improved errors/warnings
180 - consensus trees
181   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
182   - fixed NJ-bootstrapping (no longer drops species)
183 - tree display
184   - Show brackets on open groups (dendrogram tree only)
185   - rewrote IRS (folded) display
186   - fixed tree key-bindings (mark, fold, ...)
187   - improved several tree-commands (move, rotate, spread, length, width)
188 - added a branch analysis tool
189   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
190   - added leaf-distance analysis
191 - other tree functionality
192   - treelist sortable now
193   - new beautify-tree modes (radial tree / according to other tree)
194   - function to remove marked/zombies from ALL trees
195   - create multifurcations (by branchlength/bootstrap limit)
196   - toggle 100% bootstrap values
197 - tweaked printing (interface, overlapping)
198 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
199 - probe design:
200   - added LOAD to result window
201 - automation
202   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
203   - arb_ntree can execute macro from command line
204   - added "Never ask again" to modal question boxes (for better compatibility with macros)
205   - a macro can be called for all marked species (once for each)
206   - macros can be nested (i.e. can call other macros)
207 - support for user-specific customization:
208   - of GDE menus (in ~/.arb_prop/gde)
209   - of import/export filters (in ~/.arb_prop/filter)
210 - ACI (some new commands, bugfixes)
211 - updated/added external tools:
212   - added FastTree (version 2.1.7)
213   - added MAFFT (version 7.055)
214   - added MrBayes (version 3.2.1)
215   - added MUSCLE (version 3.8.31)
216   - added PHYML (2013/07/08; also kept old version 2.4.5)
217   - added PROBCONS (version 1.12)
218   - updated RAxML (version 7.7.2)
219 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
220 - Support for mouse-wheel
221 - many unlisted bugfixes
222 - many internal refactorings
223
224
225Fixes for arb_5.5 (15 Nov 2012):
226
227 * arb_5.4 was broken (several external tools missing)
228
229
230Fixes for arb_5.4 (14 Nov 2012):
231
232 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
233 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
234 * fixed several compilation issues (OSX; recent distro releases)
235
236
237Fixes for arb_5.3 (10 Nov 2011):
238
239 - bugfixes
240   - fixed wrong absolute/ecoli position reported for some designed probes
241   - decompression error handling (pt-server build issues)
242   - fixed 'codon_start' generated with wrong type
243   - fixed a buffer overflow in ACI
244   - report failures to write to /tmp
245 - changes
246   - markSpecies.pl:
247     mark by accession number
248     partial/ambiguous matches
249 - internal fixes
250   - compilation fixes for OSX
251   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
252   - removed obsolete dependency from libXp
253
254
255Fixes for arb_5.2 (5 Sep 2010):
256
257 - bugfixes
258   - quicksave did silently do nothing (especially not save anything) if an error occurred
259   - ARB_EDIT4: crashed when using config with MANY unknown species
260   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
261   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
262 - changes
263   - ARB uses xdg-open to display web-pages
264 - internal fixes
265   - karmic koala (gcc 4.4.1)
266   - installation script
267   - arb build process uses xsltproc instead of sablotron
268
269
270Fixes for arb_5.1 (1 Oct 2009):
271
272 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
273 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
274 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
275 - fixed broken demo.arb
276
277
278Major changes for arb_5.00 (4 Sep 2009):
279
280 - ARB 64bit version
281 - new genome importer
282 - search for next relatives improved (normal search and fast-aligner)
283   - new parameters to precise search
284   - improved speed
285   - partial sequence reach normal scores
286 - search&query
287   - supports regular expressions and ACI
288   - track hit information
289   - result sorting
290 - Nameservers with add.field have to be started with default value
291   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
292 - multiple PT-servers may be used in parallel
293 - fixed multiprobe
294 - type-conversion for DB fields
295 - SILVA compatible import filters
296 - Newick tree export:
297   - optionally save in human-readable format (big)
298   - closer to newick standard format (quoting style, comment, special chars in data)
299 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
300 - Fixed sequence quality calculation
301 - Secondary structures for proteins (DSSP)
302 - Distance matrix (arb_dist): mark by distance to selected
303 - ARB core
304   - many bugfixes and improvements to reliability
305   - faster sorting (general speedup)
306   - improved sequence compression (avoid worse trees, better ratio)
307   - improved handling of temporary files (permission/removal)
308   - prints backtraces in userland
309   - regular expression are POSIX standard now
310 - macro record/playback
311   - fixed several bugs
312   - you need to re-record your old macros!
313 - GUI:
314   - disabled auto-focus, you need to click now
315   - auto-raise windows on access
316 - Minor things:
317   - Ubuntu: packet installation for ARB
318   - Fixed novice/expert mode
319   - Mark deep/degenerated branches
320   - Increased NDS entries
321 - up-to-date Mac port (thx to Matt Cottrell)
322
323Major changes in ARB 07.12.07org (7 Dec 2007):
324
325 - rewrote secondary structure editor
326 - Sequence quality check
327 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
328 - tweaked base frequency filter generation
329 - Normal export (not using readseq) improved:
330   - supports filters and gap removal
331   - optimized for big amount of data
332   - reworked export filters
333 - Display translation with different ORFs in EDIT4
334 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
335 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
336 - more compact display in EDIT4
337 - capable to use iso10646 fonts
338 - supports various gcc versions (2.95.3 - 4.1.1)
339 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
340 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
341   different color for size-limited circles; fixed xfig-export-bug
342 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
343 - fixed several scaling bugs in "folded tree"-mode
344 - improved import-filter error-messages
345 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
346   several new possibilities:
347   - export taxonomy via 'Export NDS list'
348   - display taxonomy in Editor etc.
349   - display of cascaded taxonomies
350   - display taxonomy of tree_1 in tree_2
351   - allows to write taxonomy into database field of species
352   - compare taxonomies of two trees
353   - ...
354 - ACI:
355   - many new ACI commands
356   - unified handling of binary ACI-operators
357   - tracing of ACI actions for debugging purpose
358 - ARB Neighbour joining:
359   - bootstrap limit configurable
360   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
361 - EDIT4:
362   - added unalign right (block-op)
363   - added 'Save loaded properties'
364 - GENE MAP:
365   - multiple views possible at the same time
366   - origin now at "12 o'clock"
367   - implemented 'jump to gene'
368 - tweaked file selection
369 - Enhanced Search Depth for Probe Match --> max 20 MM
370 - CLUSTALW:
371   - separated menus for fast and slow alignment
372   - most parameters accessible from inside ARB now
373 - upgraded to PHYLIP 3.6 (adds PROML)
374 - external programs may be called parallel (e.g. several treeing programs)
375 - fixed bugs in protml and integration of protml
376 - rewrote ASCII database import
377 - arb_repair for databases of any size (script for database repair)
378 - fixed bug in data compression
379 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
380 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
381 - GDE menus cleanup
382 - translation/re-alignment tweaked
383 - unalign right (EDIT4)
384 - visualization of SAIs in Probe Match Results
385 - changed formatting of probe match results; increase # of allowed matches to 100.000;
386   warn if results are truncated
387 - PT server for genes
388 - Probe design performance optimized
389 - fixed NEXUS export format
390 - exports group names into Newick format
391 - import XML tree files
392 - help for external tools now properly shown inside ARB
393
394Major changes in Beta 2003_08_22 (22 Aug 2003):
395
396 - automatic formatting of alignments
397 - SECEDIT may use EDIT4 colors
398 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
399 - updated clustalw to version 1.83
400 - Restore window sizes for ALL windows (too small sizes are ignored)
401 - new algorithm to add partial sequences to an existing tree
402 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
403 - Top area of ARB_NTREE may be reduced to maximize display area
404 - All arb menus may be detached (click dashed line at top of menu)
405 - visualization of SAIs (as background color behind Sequences)
406 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
407 - PT-server occupies more memory => does less passes; more diagnostic output
408 - small changes to status window (unhide behavior/time estimation)
409 - menus and menu-hotkeys reorganized
410 - colored buttons in color config windows
411 - alignment concatenation (e.g. several different genes)
412 - merging data of similar species (according selected database field)
413 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
414 - expanded sellists
415 - save/load fixed for multi probes
416 - Binary SAIs are editable in ARB_EDIT4
417 - Information windows are detachable (allows to have multiple windows showing different items)
418 - Scanning for hidden/unknown database fields improved and separated;
419   possibility to remove unused fields.
420 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
421 - updated fastDNAml to 1.2.2
422 - added AxML (accelerated fastDNAml 1.2.2)
423 - Field transfer definitions for exporting gene-species
424 - File Selection: - recursive search available
425 - The ARB_NTREE macro recording/execution has been fixed
426 - Colorize species (see demo.arb)
427 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
428 - 'IslandHopper' -- a new integrated aligner (beta)
429 - Many improvements and bugfixes to secondary structure editor:
430   - highlighting of search (i.e for probes) like in EDIT4
431   - interactive constraint editing (stretch/compress)
432   - probe info
433   - editing secondary structure in XFIG now possible
434   - visualization of SAIs
435 - import reads Unix, DOS, and MAC linefeeds
436 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
437 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
438   (reloading of these XML files is planned for the future)
439 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
440 - search in all database fields possible ('[all fields]')
441 - up to 10 quicksaves are kept
442 - new ACI functions: upper, lower, caps, eval
443 - variables for import filter programming
444 - extract gene-species: creates acc; extraction to existing alignments
445 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
446   (=> selected gene can be highlighted in primary editor)
447 - PCR primer-design for single genes
448 - when selecting a gene, the corresponding gene-species is selected (if found)
449 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
450 - file selection box in import window
451 - mark item with double click works in all search&query windows
452 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
453 - Fixed command line help for all Arb-modules
454 - Fixed problem parsing fonts (should fix display problems with default fonts)
455 - Mark mode now works in list-view as well (ARB_NTREE)
456 - Fixed appearance of 'tiny little boxes' (everywhere)
457 - Redesign of ARB help:
458     - a HTML version is in $ARBHOME/lib/help_html
459     - a text version is in $ARBHOME/lib/help (like before, but now generated)
460
461Major changes in Beta 2001_11_07 (7 Nov 2001):
462
463 - design probes to maximum length of 60 nucleotides
464 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
465 - import default changed to foreign data format, ali name '16s'
466 - printing of multi-page-trees works again
467 - implemented user defineable masks to access database fields
468 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
469 - improved performance during pt-server-build
470 - several programs coming along with ARB where updated (PHYLIP,...)
471 - reads EMBL genom files
472 - support for experiments (genom databases only)
473
474Major changes in Beta 2001_07_24 (24 Jul 2001):
475
476 - basic support for genoms (Gene Map, reads Genebank files)
477 - ported to libc6
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