source: tags/ms_r16q3/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   * 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 - Tree shading (#443)
41   * according to values stored in database
42   * according to given topology (useful when comparing topologies)
43 - support for extra database compression (using gzip, bzip2, xz); databases cannot be opened by arb versions before 6.1.x
44 - ARB_EDIT4:
45   * display selected database fields as flags (allowing to toggle their value; #261).
46     Example use: easily mark sequence as "curated" after manually checking its alignment.
47   * allow to load missing SAIs
48   * "view differences" to a reference sequence:
49      - customizable:
50        * char used for "equality" (i.e. what is displayed where a sequence is equal to selected sequence)
51        * case-sensitivity
52        * ignore different gap-types
53      - equal data also gets hidden in consensus
54      - refresh differences of all displayed sequences, when data of selected sequences changes
55      - change reference sequence using CTRL-R or automatically let it follow the cursor
56      - added hotkey to toggle mode: CTRL-D
57      - fixed minor bugs
58   * consensus calculation in ARB_EDIT4 and calculation of CONSENSUS SAI
59     - now both calculations are strictly consistent:
60       * gaps are now ignored while deciding whether to simplify using IUPAC ambiguity codes
61       * IUPAC ambiguity codes encountered in sequence data are now counted proportionally (=> fewer 'N's occur in consensus)
62     - added sliders to consensus definition windows
63     - user defined consensus settings exchangable between both consensus setups
64     - fixed and updated documentation
65   * added species-info + database save
66 - SAI: MAX_FREQUENCY
67   * considers IUPAC ambiguity codes proportionally
68   * amino acids: if MAX_FREQUENCY is below 10% SAI now shows '1' (prev. it did show '0', i.e. 100%)
69 - expand zombies in tree (unfold groups)
70 - compare taxonomy (and mark differences; #651)
71 - external (command line) aligners:
72   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
73   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
74   * no longer ask what to do with aligned sequence, just overwrite it
75     - only warn about real sequence changes (so please do NOT ignore from now on!)
76 - config-managers:
77   * possibility to restore factory defaults
78   * added comment field for configurations
79   * added them throughout arb (#647)
80 - added slide controls throughout arb (#656)
81 - tree (display) options:
82   * fine grained scaling
83   * improved auto-jump
84   * add threshold for visible support values
85   * group shading
86   * group counters (customizable)
87   * all options are now also supported by ARB_PARSIMONY
88 - synchronized tree scrolling (#683)
89 - colorsets were invalidated by generating new IDs (#660). fixed.
90 - updated/added external tools:
91   - added alternate RAxML (DNA only; version 8.0.26)
92 - updated integrated documentation
93 - fix performance of "format sequences" (broken in arb-6.0.x series; #702)
94
95Minor changes
96 - corrected EMBL export filter (numbers at seq.data)
97 - NDS optionally uses only visible definitions
98
99Fixes for arb-6.0.5 (4 May 2016):
100
101 - fixes for ubuntu 16.04 build
102
103Fixes for arb-6.0.4 (2 May 2016):
104
105 - fixes for OSX build (SIP, accepted compilers)
106
107Fixes for arb-6.0.3 (19 Nov 2015):
108
109 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
110
111Fixes for arb-6.0.2 (8 Aug 2014):
112
113 - compile issues on Snow Leopard (OSX 10.6)
114 - merge Debian security fix for CVE-2008-5378
115 - small changes to build system for Debian
116 - add desktop integration files
117
118Fixes for arb-6.0.1 (22 Jul 2014):
119
120 - arb_parsimony
121   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
122   - corrected branchlength calculation for "Add marked partial species"
123   - 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!
124 - print
125   - preview failed (showed empty postscript file)
126   - print to file now always saves in user home
127 - raxml (import tree with bootstrap values)
128
129Major changes for arb-6.0 (4 Jun 2014):
130
131 - merge databases allows to
132   - merge from an existing database into the database loaded in ARB_NT
133   - merge to existing databases from the database loaded in ARB_NT
134 - ARB can now
135   - be restarted with another database and
136   - a second instance of ARB can be opened
137 - ARB_DIST
138   - Detect clusters of species with similar sequences (OTUs)
139   - allow automatic recalculation of matrix and/or tree whenever some parameter or
140     data changes (only makes sense for smaller species sets)
141   - extract distance matrix from tree
142 - Rewrote chimera check. Allows filtering
143 - added RNACMA (computes clusters of correlated positions)
144 - PT-Server
145   - changed behavior
146     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
147     - reports previously missing hits in joined genes
148     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
149       matches that go beyond the end of the sequence)
150     - dots in the middle of the alignment act like the sequence ends there
151     - minimum probe length reduced to 2 (was 6)
152     - allow up to 50% of probe to mismatch
153   - performance
154     - optimized memory-estimation (will build in fewer passes)
155     - uses any number of passes (not only 1, 5, 25, ...)
156     - allows to define used memory by setting environment variable ARB_MEMORY
157     - reduced memory needed to build/run ptserver (approx. 50%)
158     - reduced size of indexfile (.pt) to ~50%
159     - fast startup of existing ptservers
160   - probe design
161     - faster in many cases
162     - allow to design probes of length 8 (previously 10)
163     - allow to design probes with different lengths (specifying min/max length)
164     - fixed number of outgroup hits reported when decreasing temperature
165       (now each outgroup member only occurs once)
166     - show possible reasons why no probes could be designed
167   - probe match (allow any number of mismatches)
168   - next relative search
169     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
170     - corrected and improved scaling of relative scores
171     - more accurate scores (due to fixes in PT-Server; see below)
172     - faster in many cases
173   - show errors from ptserver build in ARB
174 - fast-aligner
175   - searches next-relatives based on selected column-block
176   - align multiple column-blocks based on SAI
177 - Rewrote alignment adaption during merge
178 - Insert/delete columns using a SAI to define affected columns
179 - ARB_EDIT4
180   - improved support for using multiple edit-windows
181   - smoother refreshes
182   - tweaked ORF display
183 - tree importer/exporter
184   - ARBs extended newick format (with bootstrap values) handled more restrictive now
185   - fixed several bugs; improved errors/warnings
186 - consensus trees
187   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
188   - fixed NJ-bootstrapping (no longer drops species)
189 - tree display
190   - Show brackets on open groups (dendrogram tree only)
191   - rewrote IRS (folded) display
192   - fixed tree key-bindings (mark, fold, ...)
193   - improved several tree-commands (move, rotate, spread, length, width)
194 - added a branch analysis tool
195   - groups several functions previously available via menuitems (e.g. mark long branches, etc.)
196   - added leaf-distance analysis
197 - other tree functionality
198   - treelist sortable now
199   - new beautify-tree modes (radial tree / according to other tree)
200   - function to remove marked/zombies from ALL trees
201   - create multifurcations (by branchlength/bootstrap limit)
202   - toggle 100% bootstrap values
203 - tweaked printing (interface, overlapping)
204 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
205 - probe design:
206   - added LOAD to result window
207 - automation
208   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
209   - arb_ntree can execute macro from command line
210   - added "Never ask again" to modal question boxes (for better compatibility with macros)
211   - a macro can be called for all marked species (once for each)
212   - macros can be nested (i.e. can call other macros)
213 - support for user-specific customization:
214   - of GDE menus (in ~/.arb_prop/gde)
215   - of import/export filters (in ~/.arb_prop/filter)
216 - ACI (some new commands, bugfixes)
217 - updated/added external tools:
218   - added FastTree (version 2.1.7)
219   - added MAFFT (version 7.055)
220   - added MrBayes (version 3.2.1)
221   - added MUSCLE (version 3.8.31)
222   - added PHYML (2013/07/08; also kept old version 2.4.5)
223   - added PROBCONS (version 1.12)
224   - updated RAxML (version 7.7.2)
225 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
226 - Support for mouse-wheel
227 - many unlisted bugfixes
228 - many internal refactorings
229
230
231Fixes for arb_5.5 (15 Nov 2012):
232
233 * arb_5.4 was broken (several external tools missing)
234
235
236Fixes for arb_5.4 (14 Nov 2012):
237
238 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
239 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
240 * fixed several compilation issues (OSX; recent distro releases)
241
242
243Fixes for arb_5.3 (10 Nov 2011):
244
245 - bugfixes
246   - fixed wrong absolute/ecoli position reported for some designed probes
247   - decompression error handling (pt-server build issues)
248   - fixed 'codon_start' generated with wrong type
249   - fixed a buffer overflow in ACI
250   - report failures to write to /tmp
251 - changes
252   - markSpecies.pl:
253     mark by accession number
254     partial/ambiguous matches
255 - internal fixes
256   - compilation fixes for OSX
257   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
258   - removed obsolete dependency from libXp
259
260
261Fixes for arb_5.2 (5 Sep 2010):
262
263 - bugfixes
264   - quicksave did silently do nothing (especially not save anything) if an error occurred
265   - ARB_EDIT4: crashed when using config with MANY unknown species
266   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
267   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
268 - changes
269   - ARB uses xdg-open to display web-pages
270 - internal fixes
271   - karmic koala (gcc 4.4.1)
272   - installation script
273   - arb build process uses xsltproc instead of sablotron
274
275
276Fixes for arb_5.1 (1 Oct 2009):
277
278 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
279 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
280 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
281 - fixed broken demo.arb
282
283
284Major changes for arb_5.00 (4 Sep 2009):
285
286 - ARB 64bit version
287 - new genome importer
288 - search for next relatives improved (normal search and fast-aligner)
289   - new parameters to precise search
290   - improved speed
291   - partial sequence reach normal scores
292 - search&query
293   - supports regular expressions and ACI
294   - track hit information
295   - result sorting
296 - Nameservers with add.field have to be started with default value
297   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
298 - multiple PT-servers may be used in parallel
299 - fixed multiprobe
300 - type-conversion for DB fields
301 - SILVA compatible import filters
302 - Newick tree export:
303   - optionally save in human-readable format (big)
304   - closer to newick standard format (quoting style, comment, special chars in data)
305 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
306 - Fixed sequence quality calculation
307 - Secondary structures for proteins (DSSP)
308 - Distance matrix (arb_dist): mark by distance to selected
309 - ARB core
310   - many bugfixes and improvements to reliability
311   - faster sorting (general speedup)
312   - improved sequence compression (avoid worse trees, better ratio)
313   - improved handling of temporary files (permission/removal)
314   - prints backtraces in userland
315   - regular expression are POSIX standard now
316 - macro record/playback
317   - fixed several bugs
318   - you need to re-record your old macros!
319 - GUI:
320   - disabled auto-focus, you need to click now
321   - auto-raise windows on access
322 - Minor things:
323   - Ubuntu: packet installation for ARB
324   - Fixed novice/expert mode
325   - Mark deep/degenerated branches
326   - Increased NDS entries
327 - up-to-date Mac port (thx to Matt Cottrell)
328
329Major changes in ARB 07.12.07org (7 Dec 2007):
330
331 - rewrote secondary structure editor
332 - Sequence quality check
333 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
334 - tweaked base frequency filter generation
335 - Normal export (not using readseq) improved:
336   - supports filters and gap removal
337   - optimized for big amount of data
338   - reworked export filters
339 - Display translation with different ORFs in EDIT4
340 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
341 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
342 - more compact display in EDIT4
343 - capable to use iso10646 fonts
344 - supports various gcc versions (2.95.3 - 4.1.1)
345 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
346 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
347   different color for size-limited circles; fixed xfig-export-bug
348 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
349 - fixed several scaling bugs in "folded tree"-mode
350 - improved import-filter error-messages
351 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
352   several new possibilities:
353   - export taxonomy via 'Export NDS list'
354   - display taxonomy in Editor etc.
355   - display of cascaded taxonomies
356   - display taxonomy of tree_1 in tree_2
357   - allows to write taxonomy into database field of species
358   - compare taxonomies of two trees
359   - ...
360 - ACI:
361   - many new ACI commands
362   - unified handling of binary ACI-operators
363   - tracing of ACI actions for debugging purpose
364 - ARB Neighbour joining:
365   - bootstrap limit configurable
366   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
367 - EDIT4:
368   - added unalign right (block-op)
369   - added 'Save loaded properties'
370 - GENE MAP:
371   - multiple views possible at the same time
372   - origin now at "12 o'clock"
373   - implemented 'jump to gene'
374 - tweaked file selection
375 - Enhanced Search Depth for Probe Match --> max 20 MM
376 - CLUSTALW:
377   - separated menus for fast and slow alignment
378   - most parameters accessible from inside ARB now
379 - upgraded to PHYLIP 3.6 (adds PROML)
380 - external programs may be called parallel (e.g. several treeing programs)
381 - fixed bugs in protml and integration of protml
382 - rewrote ASCII database import
383 - arb_repair for databases of any size (script for database repair)
384 - fixed bug in data compression
385 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
386 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
387 - GDE menus cleanup
388 - translation/re-alignment tweaked
389 - unalign right (EDIT4)
390 - visualization of SAIs in Probe Match Results
391 - changed formatting of probe match results; increase # of allowed matches to 100.000;
392   warn if results are truncated
393 - PT server for genes
394 - Probe design performance optimized
395 - fixed NEXUS export format
396 - exports group names into Newick format
397 - import XML tree files
398 - help for external tools now properly shown inside ARB
399
400Major changes in Beta 2003_08_22 (22 Aug 2003):
401
402 - automatic formatting of alignments
403 - SECEDIT may use EDIT4 colors
404 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
405 - updated clustalw to version 1.83
406 - Restore window sizes for ALL windows (too small sizes are ignored)
407 - new algorithm to add partial sequences to an existing tree
408 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
409 - Top area of ARB_NTREE may be reduced to maximize display area
410 - All arb menus may be detached (click dashed line at top of menu)
411 - visualization of SAIs (as background color behind Sequences)
412 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
413 - PT-server occupies more memory => does less passes; more diagnostic output
414 - small changes to status window (unhide behavior/time estimation)
415 - menus and menu-hotkeys reorganized
416 - colored buttons in color config windows
417 - alignment concatenation (e.g. several different genes)
418 - merging data of similar species (according selected database field)
419 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
420 - expanded sellists
421 - save/load fixed for multi probes
422 - Binary SAIs are editable in ARB_EDIT4
423 - Information windows are detachable (allows to have multiple windows showing different items)
424 - Scanning for hidden/unknown database fields improved and separated;
425   possibility to remove unused fields.
426 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
427 - updated fastDNAml to 1.2.2
428 - added AxML (accelerated fastDNAml 1.2.2)
429 - Field transfer definitions for exporting gene-species
430 - File Selection: - recursive search available
431 - The ARB_NTREE macro recording/execution has been fixed
432 - Colorize species (see demo.arb)
433 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
434 - 'IslandHopper' -- a new integrated aligner (beta)
435 - Many improvements and bugfixes to secondary structure editor:
436   - highlighting of search (i.e for probes) like in EDIT4
437   - interactive constraint editing (stretch/compress)
438   - probe info
439   - editing secondary structure in XFIG now possible
440   - visualization of SAIs
441 - import reads Unix, DOS, and MAC linefeeds
442 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
443 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
444   (reloading of these XML files is planned for the future)
445 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
446 - search in all database fields possible ('[all fields]')
447 - up to 10 quicksaves are kept
448 - new ACI functions: upper, lower, caps, eval
449 - variables for import filter programming
450 - extract gene-species: creates acc; extraction to existing alignments
451 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
452   (=> selected gene can be highlighted in primary editor)
453 - PCR primer-design for single genes
454 - when selecting a gene, the corresponding gene-species is selected (if found)
455 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
456 - file selection box in import window
457 - mark item with double click works in all search&query windows
458 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
459 - Fixed command line help for all Arb-modules
460 - Fixed problem parsing fonts (should fix display problems with default fonts)
461 - Mark mode now works in list-view as well (ARB_NTREE)
462 - Fixed appearance of 'tiny little boxes' (everywhere)
463 - Redesign of ARB help:
464     - a HTML version is in $ARBHOME/lib/help_html
465     - a text version is in $ARBHOME/lib/help (like before, but now generated)
466
467Major changes in Beta 2001_11_07 (7 Nov 2001):
468
469 - design probes to maximum length of 60 nucleotides
470 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
471 - import default changed to foreign data format, ali name '16s'
472 - printing of multi-page-trees works again
473 - implemented user defineable masks to access database fields
474 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
475 - improved performance during pt-server-build
476 - several programs coming along with ARB where updated (PHYLIP,...)
477 - reads EMBL genom files
478 - support for experiments (genom databases only)
479
480Major changes in Beta 2001_07_24 (24 Jul 2001):
481
482 - basic support for genoms (Gene Map, reads Genebank files)
483 - ported to libc6
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