source: branches/profile/arb_CHANGES.txt

Last change on this file was 12925, checked in by westram, 5 years ago
  • mention raxml8 + expand zombies
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1ARB change log
2
3Major changes for next release:
4
5 - DNA realigner
6   * several unjustified failures will no longer happen (fixes #419 and most likely #145)
7     - correctly re-syncs after 'X' (if possible at all)
8     - no longer fails for 'B' and 'Z'
9     - accepts 3 or more consecutive IUPAC codes in DNA
10   * added option to cut-off DNA sequence (was done at end of sequence by old version. fixed)
11   * fixed several minor bugs
12 - expand zombies in tree (unfold groups)
13 - external (command line) aligners:
14   * fixed incorrect handling of 'T' vs 'U': now all aligned sequences will contain the correct base depending on alignment type
15   * preserve gap-type ('-' vs '.') and upper-/lower-case of original alignment
16   * no longer ask what to do with aligned sequence, just overwrite it
17     - only warn about real sequence changes (so please do NOT ignore from now on!)
18 - updated/added external tools:
19   - added alternate RAxML (DNA only; version 8.0.26)
20
21Fixes for arb-6.0.2 (8 Aug 2014):
22
23 - compile issues on Snow Leopard (OSX 10.6)
24 - merge Debian security fix for CVE-2008-5378
25 - small changes to build system for Debian
26 - add desktop integration files
27
28Fixes for arb-6.0.1 (22 Jul 2014):
29
30 - arb_parsimony
31   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
32   - corrected branchlength calculation for "Add marked partial species"
33   - 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!
34 - print
35   - preview failed (showed empty postscript file)
36   - print to file now always saves in user home
37 - raxml (import tree with bootstrap values)
38
39
40Major changes for arb-6.0 (4 Jun 2014):
41
42 - merge databases allows to
43   - merge from an existing database into the database loaded in ARB_NT
44   - merge to existing databases from the database loaded in ARB_NT
45 - ARB can now
46   - be restarted with another database and
47   - a second instance of ARB can be opened
48 - ARB_DIST
49   - Detect clusters of species with similar sequences (OTUs)
50   - allow automatic recalculation of matrix and/or tree whenever some parameter or
51     data changes (only makes sense for smaller species sets)
52   - extract distance matrix from tree
53 - Rewrote chimera check. Allows filtering
54 - added RNACMA (computes clusters of correlated positions)
55 - PT-Server
56   - changed behavior
57     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
58     - reports previously missing hits in joined genes
59     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
60       matches that go beyond the end of the sequence)
61     - dots in the middle of the alignment act like the sequence ends there
62     - minimum probe length reduced to 2 (was 6)
63     - allow up to 50% of probe to mismatch
64   - performance
65     - optimized memory-estimation (will build in fewer passes)
66     - uses any number of passes (not only 1, 5, 25, ...)
67     - allows to define used memory by setting environment variable ARB_MEMORY
68     - reduced memory needed to build/run ptserver (approx. 50%)
69     - reduced size of indexfile (.pt) to ~50%
70     - fast startup of existing ptservers
71   - probe design
72     - faster in many cases
73     - allow to design probes of length 8 (previously 10)
74     - allow to design probes with different lengths (specifying min/max length)
75     - fixed number of outgroup hits reported when decreasing temperature
76       (now each outgroup member only occurs once)
77     - show possible reasons why no probes could be designed
78   - probe match (allow any number of mismatches)
79   - next relative search
80     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
81     - corrected and improved scaling of relative scores
82     - more accurate scores (due to fixes in PT-Server; see below)
83     - faster in many cases
84   - show errors from ptserver build in ARB
85 - fast-aligner
86   - searches next-relatives based on selected column-block
87   - align multiple column-blocks based on SAI
88 - Rewrote alignment adaption during merge
89 - Insert/delete columns using a SAI to define affected columns
90 - ARB_EDIT4
91   - improved support for using multiple edit-windows
92   - smoother refreshes
93   - tweaked ORF display
94 - tree importer/exporter
95   - ARBs extended newick format (with bootstrap values) handled more restrictive now
96   - fixed several bugs; improved errors/warnings
97 - consensus trees
98   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
99   - fixed NJ-bootstrapping (no longer drops species)
100 - tree display
101   - Show brackets on open groups (dendrogram tree only)
102   - rewrote IRS (folded) display
103   - fixed tree key-bindings (mark, fold, ...)
104   - improved several tree-commands (move, rotate, spread, length, width)
105 - added a branch analysis tool
106   - groups several functions previously availiable via menuitems (e.g. mark long branches, etc.)
107   - added leaf-distance analysis
108 - other tree functionality
109   - treelist sortable now
110   - new beautify-tree modes (radial tree / according to other tree)
111   - function to remove marked/zombies from ALL trees
112   - create multifurcations (by branchlength/bootstrap limit)
113   - toggle 100% bootstrap values
114 - tweaked printing (interface, overlapping)
115 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
116 - probe design:
117   - added LOAD to result window
118 - automation
119   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
120   - arb_ntree can execute macro from command line
121   - added "Never ask again" to modal question boxes (for better compatibility with macros)
122   - a macro can be called for all marked species (once for each)
123   - macros can be nested (i.e. can call other macros)
124 - support for user-specific customization:
125   - of GDE menus (in ~/.arb_prop/gde)
126   - of import/export filters (in ~/.arb_prop/filter)
127 - ACI (some new commands, bugfixes)
128 - updated/added external tools:
129   - added FastTree (version 2.1.7)
130   - added MAFFT (version 7.055)
131   - added MrBayes (version 3.2.1)
132   - added MUSCLE (version 3.8.31)
133   - added PHYML (2013/07/08; also kept old version 2.4.5)
134   - added PROBCONS (version 1.12)
135   - updated RAxML (version 7.7.2)
136 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
137 - Support for mouse-wheel
138 - many unlisted bugfixes
139 - many internal refactorings
140
141
142Fixes for arb_5.5 (15 Nov 2012):
143
144 * arb_5.4 was broken (several external tools missing)
145
146
147Fixes for arb_5.4 (14 Nov 2012):
148
149 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
150 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
151 * fixed several compilation issues (OSX; recent distro releases)
152
153
154Fixes for arb_5.3 (10 Nov 2011):
155
156 - bugfixes
157   - fixed wrong absolute/ecoli position reported for some designed probes
158   - decompression error handling (pt-server build issues)
159   - fixed 'codon_start' generated with wrong type
160   - fixed a buffer overflow in ACI
161   - report failures to write to /tmp
162 - changes
163   - markSpecies.pl:
164     mark by accession number
165     partial/ambiguous matches
166 - internal fixes
167   - compilation fixes for OSX
168   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
169   - removed obsolete dependency from libXp
170
171
172Fixes for arb_5.2 (5 Sep 2010):
173
174 - bugfixes
175   - quicksave did silently do nothing (especially not save anything) if an error occurred
176   - ARB_EDIT4: crashed when using config with MANY unknown species
177   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
178   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
179 - changes
180   - ARB uses xdg-open to display web-pages
181 - internal fixes
182   - karmic koala (gcc 4.4.1)
183   - installation script
184   - arb build process uses xsltproc instead of sablotron
185
186
187Fixes for arb_5.1 (1 Oct 2009):
188
189 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
190 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
191 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
192 - fixed broken demo.arb
193
194
195Major changes for arb_5.00 (4 Sep 2009):
196
197 - ARB 64bit version
198 - new genome importer
199 - search for next relatives improved (normal search and fast-aligner)
200   - new parameters to precise search
201   - improved speed
202   - partial sequence reach normal scores
203 - search&query
204   - supports regular expressions and ACI
205   - track hit information
206   - result sorting
207 - Nameservers with add.field have to be started with default value
208   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
209 - multiple PT-servers may be used in parallel
210 - fixed multiprobe
211 - type-conversion for DB fields
212 - SILVA compatible import filters
213 - Newick tree export:
214   - optionally save in human-readable format (big)
215   - closer to newick standard format (quoting style, comment, special chars in data)
216 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
217 - Fixed sequence quality calculation
218 - Secondary structures for proteins (DSSP)
219 - Distance matrix (arb_dist): mark by distance to selected
220 - ARB core
221   - many bugfixes and improvements to reliability
222   - faster sorting (general speedup)
223   - improved sequence compression (avoid worse trees, better ratio)
224   - improved handling of temporary files (permission/removal)
225   - prints backtraces in userland
226   - regular expression are POSIX standard now
227 - macro record/playback
228   - fixed several bugs
229   - you need to re-record your old macros!
230 - GUI:
231   - disabled auto-focus, you need to click now
232   - auto-raise windows on access
233 - Minor things:
234   - Ubuntu: packet installation for ARB
235   - Fixed novice/expert mode
236   - Mark deep/degenerated branches
237   - Increased NDS entries
238 - up-to-date Mac port (thx to Matt Cottrell)
239
240Major changes in ARB 07.12.07org (7 Dec 2007):
241
242 - rewrote secondary structure editor
243 - Sequence quality check
244 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
245 - tweaked base frequency filter generation
246 - Normal export (not using readseq) improved:
247   - supports filters and gap removal
248   - optimized for big amount of data
249   - reworked export filters
250 - Display translation with different ORFs in EDIT4
251 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
252 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
253 - more compact display in EDIT4
254 - capable to use iso10646 fonts
255 - supports various gcc versions (2.95.3 - 4.1.1)
256 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
257 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
258   different color for size-limited circles; fixed xfig-export-bug
259 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
260 - fixed several scaling bugs in "folded tree"-mode
261 - improved import-filter error-messages
262 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
263   several new possibilities:
264   - export taxonomy via 'Export NDS list'
265   - display taxonomy in Editor etc.
266   - display of cascaded taxonomies
267   - display taxonomy of tree_1 in tree_2
268   - allows to write taxonomy into database field of species
269   - compare taxonomies of two trees
270   - ...
271 - ACI:
272   - many new ACI commands
273   - unified handling of binary ACI-operators
274   - tracing of ACI actions for debugging purpose
275 - ARB Neighbour joining:
276   - bootstrap limit configurable
277   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
278 - EDIT4:
279   - added unalign right (block-op)
280   - added 'Save loaded properties'
281 - GENE MAP:
282   - multiple views possible at the same time
283   - origin now at "12 o'clock"
284   - implemented 'jump to gene'
285 - tweaked file selection
286 - Enhanced Search Depth for Probe Match --> max 20 MM
287 - CLUSTALW:
288   - separated menus for fast and slow alignment
289   - most parameters accessible from inside ARB now
290 - upgraded to PHYLIP 3.6 (adds PROML)
291 - external programs may be called parallel (e.g. several treeing programs)
292 - fixed bugs in protml and integration of protml
293 - rewrote ASCII database import
294 - arb_repair for databases of any size (script for database repair)
295 - fixed bug in data compression
296 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
297 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
298 - GDE menus cleanup
299 - translation/re-alignment tweaked
300 - unalign right (EDIT4)
301 - visualization of SAIs in Probe Match Results
302 - changed formatting of probe match results; increase # of allowed matches to 100.000;
303   warn if results are truncated
304 - PT server for genes
305 - Probe design performance optimized
306 - fixed NEXUS export format
307 - exports group names into Newick format
308 - import XML tree files
309 - help for external tools now properly shown inside ARB
310
311Major changes in Beta 2003_08_22 (22 Aug 2003):
312
313 - automatic formatting of alignments
314 - SECEDIT may use EDIT4 colors
315 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
316 - updated clustalw to version 1.83
317 - Restore window sizes for ALL windows (too small sizes are ignored)
318 - new algorithm to add partial sequences to an existing tree
319 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
320 - Top area of ARB_NTREE may be reduced to maximize display area
321 - All arb menus may be detached (click dashed line at top of menu)
322 - visualization of SAIs (as background color behind Sequences)
323 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
324 - PT-server occupies more memory => does less passes; more diagnostic output
325 - small changes to status window (unhide behavior/time estimation)
326 - menus and menu-hotkeys reorganized
327 - colored buttons in color config windows
328 - alignment concatenation (e.g. several different genes)
329 - merging data of similar species (according selected database field)
330 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
331 - expanded sellists
332 - save/load fixed for multi probes
333 - Binary SAIs are editable in ARB_EDIT4
334 - Information windows are detachable (allows to have multiple windows showing different items)
335 - Scanning for hidden/unknown database fields improved and separated;
336   possibility to remove unused fields.
337 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
338 - updated fastDNAml to 1.2.2
339 - added AxML (accelerated fastDNAml 1.2.2)
340 - Field transfer definitions for exporting gene-species
341 - File Selection: - recursive search available
342 - The ARB_NTREE macro recording/execution has been fixed
343 - Colorize species (see demo.arb)
344 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
345 - 'IslandHopper' -- a new integrated aligner (beta)
346 - Many improvements and bugfixes to secondary structure editor:
347   - highlighting of search (i.e for probes) like in EDIT4
348   - interactive constraint editing (stretch/compress)
349   - probe info
350   - editing secondary structure in XFIG now possible
351   - visualization of SAIs
352 - import reads Unix, DOS, and MAC linefeeds
353 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
354 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
355   (reloading of these XML files is planned for the future)
356 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
357 - search in all database fields possible ('[all fields]')
358 - up to 10 quicksaves are kept
359 - new ACI functions: upper, lower, caps, eval
360 - variables for import filter programming
361 - extract gene-species: creates acc; extraction to existing alignments
362 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
363   (=> selected gene can be highlighted in primary editor)
364 - PCR primer-design for single genes
365 - when selecting a gene, the corresponding gene-species is selected (if found)
366 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
367 - file selection box in import window
368 - mark item with double click works in all search&query windows
369 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
370 - Fixed command line help for all Arb-modules
371 - Fixed problem parsing fonts (should fix display problems with default fonts)
372 - Mark mode now works in list-view as well (ARB_NTREE)
373 - Fixed appearance of 'tiny little boxes' (everywhere)
374 - Redesign of ARB help:
375     - a HTML version is in $ARBHOME/lib/help_html
376     - a text version is in $ARBHOME/lib/help (like before, but now generated)
377
378Major changes in Beta 2001_11_07 (7 Nov 2001):
379
380 - design probes to maximum length of 60 nucleotides
381 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
382 - import default changed to foreign data format, ali name '16s'
383 - printing of multi-page-trees works again
384 - implemented user defineable masks to access database fields
385 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
386 - improved performance during pt-server-build
387 - several programs coming along with ARB where updated (PHYLIP,...)
388 - reads EMBL genom files
389 - support for experiments (genom databases only)
390
391Major changes in Beta 2001_07_24 (24 Jul 2001):
392
393 - basic support for genoms (Gene Map, reads Genebank files)
394 - ported to libc6
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