source: branches/stable/arb_CHANGES.txt

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1ARB change log
2
3Fixes for arb-6.0.6 (22 Aug 2016):
4
5 - fixes for gcc 6.1.0
6 - tested gcc 4.9.4 + 5.4.0
7
8Fixes for arb-6.0.5 (4 May 2016):
9
10 - fixes for ubuntu 16.04 build
11
12Fixes for arb-6.0.4 (2 May 2016):
13
14 - fixes for OSX build (SIP, accepted compilers)
15
16Fixes for arb-6.0.3 (19 Nov 2015):
17
18 - fixes permission problems when multiple users share databases or ptservers (thx to Alan McCulloch)
19
20Fixes for arb-6.0.2 (8 Aug 2014):
21
22 - compile issues on Snow Leopard (OSX 10.6)
23 - merge Debian security fix for CVE-2008-5378
24 - small changes to build system for Debian
25 - add desktop integration files
26
27Fixes for arb-6.0.1 (22 Jul 2014):
28
29 - arb_parsimony
30   - skip unwanted automatic branchlength recalculations (e.g. by unfolding a group)
31   - corrected branchlength calculation for "Add marked partial species"
32   - 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!
33 - print
34   - preview failed (showed empty postscript file)
35   - print to file now always saves in user home
36 - raxml (import tree with bootstrap values)
37
38Major changes for arb-6.0 (4 Jun 2014):
39
40 - merge databases allows to
41   - merge from an existing database into the database loaded in ARB_NT
42   - merge to existing databases from the database loaded in ARB_NT
43 - ARB can now
44   - be restarted with another database and
45   - a second instance of ARB can be opened
46 - ARB_DIST
47   - Detect clusters of species with similar sequences (OTUs)
48   - allow automatic recalculation of matrix and/or tree whenever some parameter or
49     data changes (only makes sense for smaller species sets)
50   - extract distance matrix from tree
51 - Rewrote chimera check. Allows filtering
52 - added RNACMA (computes clusters of correlated positions)
53 - PT-Server
54   - changed behavior
55     - no longer report less hits for a part of a probe than for the probe itself (occurred at 3'-end of alignment)
56     - reports previously missing hits in joined genes
57     - reports more hits at 3'-end of alignment (when using mismatches the PT-server now reports possible
58       matches that go beyond the end of the sequence)
59     - dots in the middle of the alignment act like the sequence ends there
60     - minimum probe length reduced to 2 (was 6)
61     - allow up to 50% of probe to mismatch
62   - performance
63     - optimized memory-estimation (will build in fewer passes)
64     - uses any number of passes (not only 1, 5, 25, ...)
65     - allows to define used memory by setting environment variable ARB_MEMORY
66     - reduced memory needed to build/run ptserver (approx. 50%)
67     - reduced size of indexfile (.pt) to ~50%
68     - fast startup of existing ptservers
69   - probe design
70     - faster in many cases
71     - allow to design probes of length 8 (previously 10)
72     - allow to design probes with different lengths (specifying min/max length)
73     - fixed number of outgroup hits reported when decreasing temperature
74       (now each outgroup member only occurs once)
75     - show possible reasons why no probes could be designed
76   - probe match (allow any number of mismatches)
77   - next relative search
78     - can be restricted to column ranges (needs a PT-Server calculated from aligned sequences)
79     - corrected and improved scaling of relative scores
80     - more accurate scores (due to fixes in PT-Server; see below)
81     - faster in many cases
82   - show errors from ptserver build in ARB
83 - fast-aligner
84   - searches next-relatives based on selected column-block
85   - align multiple column-blocks based on SAI
86 - Rewrote alignment adaption during merge
87 - Insert/delete columns using a SAI to define affected columns
88 - ARB_EDIT4
89   - improved support for using multiple edit-windows
90   - smoother refreshes
91   - tweaked ORF display
92 - tree importer/exporter
93   - ARBs extended newick format (with bootstrap values) handled more restrictive now
94   - fixed several bugs; improved errors/warnings
95 - consensus trees
96   - calculate from multiple existing trees (also allows to merge not completely overlapping trees)
97   - fixed NJ-bootstrapping (no longer drops species)
98 - tree display
99   - Show brackets on open groups (dendrogram tree only)
100   - rewrote IRS (folded) display
101   - fixed tree key-bindings (mark, fold, ...)
102   - improved several tree-commands (move, rotate, spread, length, width)
103 - added a branch analysis tool
104   - groups several functions previously availiable via menuitems (e.g. mark long branches, etc.)
105   - added leaf-distance analysis
106 - other tree functionality
107   - treelist sortable now
108   - new beautify-tree modes (radial tree / according to other tree)
109   - function to remove marked/zombies from ALL trees
110   - create multifurcations (by branchlength/bootstrap limit)
111   - toggle 100% bootstrap values
112 - tweaked printing (interface, overlapping)
113 - if YOU edit a helpfile it will be automatically packed into an archive ready to be sent to ARB developers
114 - probe design:
115   - added LOAD to result window
116 - automation
117   - macro recording works in ARB client applications (ARB_EDIT4, ARB_PARS, ARB_MERGE, ..)
118   - arb_ntree can execute macro from command line
119   - added "Never ask again" to modal question boxes (for better compatibility with macros)
120   - a macro can be called for all marked species (once for each)
121   - macros can be nested (i.e. can call other macros)
122 - support for user-specific customization:
123   - of GDE menus (in ~/.arb_prop/gde)
124   - of import/export filters (in ~/.arb_prop/filter)
125 - ACI (some new commands, bugfixes)
126 - updated/added external tools:
127   - added FastTree (version 2.1.7)
128   - added MAFFT (version 7.055)
129   - added MrBayes (version 3.2.1)
130   - added MUSCLE (version 3.8.31)
131   - added PHYML (2013/07/08; also kept old version 2.4.5)
132   - added PROBCONS (version 1.12)
133   - updated RAxML (version 7.7.2)
134 - load/save for window specific settings (e.g. allows to share parts of configuration with other users)
135 - Support for mouse-wheel
136 - many unlisted bugfixes
137 - many internal refactorings
138
139
140Fixes for arb_5.5 (15 Nov 2012):
141
142 * arb_5.4 was broken (several external tools missing)
143
144
145Fixes for arb_5.4 (14 Nov 2012):
146
147 * make it obvious when probe matches are truncated. Truncate all hits beyond 1 million (was 100000)
148 * fixed realigner (better interaction with fields 'transl_table' and 'codon_start'; improved error handling)
149 * fixed several compilation issues (OSX; recent distro releases)
150
151
152Fixes for arb_5.3 (10 Nov 2011):
153
154 - bugfixes
155   - fixed wrong absolute/ecoli position reported for some designed probes
156   - decompression error handling (pt-server build issues)
157   - fixed 'codon_start' generated with wrong type
158   - fixed a buffer overflow in ACI
159   - report failures to write to /tmp
160 - changes
161   - markSpecies.pl:
162     mark by accession number
163     partial/ambiguous matches
164 - internal fixes
165   - compilation fixes for OSX
166   - some patches for debian version (removed refs to xview, textedit, removed molphy(protml))
167   - removed obsolete dependency from libXp
168
169
170Fixes for arb_5.2 (5 Sep 2010):
171
172 - bugfixes
173   - quicksave did silently do nothing (especially not save anything) if an error occurred
174   - ARB_EDIT4: crashed when using config with MANY unknown species
175   - ARB_SECEDIT: crashed when trying to paint strand w/o any base
176   - ARB_NTREE/ARB_PARS: crashed when clicking on inner tree node w/o groupinfo
177 - changes
178   - ARB uses xdg-open to display web-pages
179 - internal fixes
180   - karmic koala (gcc 4.4.1)
181   - installation script
182   - arb build process uses xsltproc instead of sablotron
183
184
185Fixes for arb_5.1 (1 Oct 2009):
186
187 - fixed a bug in 'Create species from consensus' (created sequence was corrupted)
188 - fixed 2 bugs in optimize DB (alignment w/o data, missing transaction)
189 - updated installation instructions, fixed install script, added OSX instruction (thx to Matt Cottrell)
190 - fixed broken demo.arb
191
192
193Major changes for arb_5.00 (4 Sep 2009):
194
195 - ARB 64bit version
196 - new genome importer
197 - search for next relatives improved (normal search and fast-aligner)
198   - new parameters to precise search
199   - improved speed
200   - partial sequence reach normal scores
201 - search&query
202   - supports regular expressions and ACI
203   - track hit information
204   - result sorting
205 - Nameservers with add.field have to be started with default value
206   You need to correct parameter -f in lib/arb_tcp.dat (according to lib/arb_tcp_org.dat)
207 - multiple PT-servers may be used in parallel
208 - fixed multiprobe
209 - type-conversion for DB fields
210 - SILVA compatible import filters
211 - Newick tree export:
212   - optionally save in human-readable format (big)
213   - closer to newick standard format (quoting style, comment, special chars in data)
214 - Upgraded RAxML to 7.0.3 (many features now usable from ARB interface)
215 - Fixed sequence quality calculation
216 - Secondary structures for proteins (DSSP)
217 - Distance matrix (arb_dist): mark by distance to selected
218 - ARB core
219   - many bugfixes and improvements to reliability
220   - faster sorting (general speedup)
221   - improved sequence compression (avoid worse trees, better ratio)
222   - improved handling of temporary files (permission/removal)
223   - prints backtraces in userland
224   - regular expression are POSIX standard now
225 - macro record/playback
226   - fixed several bugs
227   - you need to re-record your old macros!
228 - GUI:
229   - disabled auto-focus, you need to click now
230   - auto-raise windows on access
231 - Minor things:
232   - Ubuntu: packet installation for ARB
233   - Fixed novice/expert mode
234   - Mark deep/degenerated branches
235   - Increased NDS entries
236 - up-to-date Mac port (thx to Matt Cottrell)
237
238Major changes in ARB 07.12.07org (7 Dec 2007):
239
240 - rewrote secondary structure editor
241 - Sequence quality check
242 - Nameserver may use one field additional to 'acc' (useful to keep multiple species with same acc)
243 - tweaked base frequency filter generation
244 - Normal export (not using readseq) improved:
245   - supports filters and gap removal
246   - optimized for big amount of data
247   - reworked export filters
248 - Display translation with different ORFs in EDIT4
249 - ARB exports in FIG 3.2 format (optionally in colors). Thanks to Elmar Pruesse.
250 - added PHYML 2.4.5 (thanks to Stephane Guidon for the permission to distribute that great tool)
251 - more compact display in EDIT4
252 - capable to use iso10646 fonts
253 - supports various gcc versions (2.95.3 - 4.1.1)
254 - fixed a bug in DB optimization (occurred when fields had bigger protection than current)
255 - Bootstrap circles may be displayed as ellipses; upper size limit configurable; uses
256   different color for size-limited circles; fixed xfig-export-bug
257 - Allows Branchlength <-> Bootstrap value transfer (lossy!)
258 - fixed several scaling bugs in "folded tree"-mode
259 - improved import-filter error-messages
260 - NDS-display of groups (e.g. in tree) is now handled by ACI-command 'taxonomy'. This gives
261   several new possibilities:
262   - export taxonomy via 'Export NDS list'
263   - display taxonomy in Editor etc.
264   - display of cascaded taxonomies
265   - display taxonomy of tree_1 in tree_2
266   - allows to write taxonomy into database field of species
267   - compare taxonomies of two trees
268   - ...
269 - ACI:
270   - many new ACI commands
271   - unified handling of binary ACI-operators
272   - tracing of ACI actions for debugging purpose
273 - ARB Neighbour joining:
274   - bootstrap limit configurable
275   - bugfix: when aborting bootstrap calculation, sometimes no tree was generated
276 - EDIT4:
277   - added unalign right (block-op)
278   - added 'Save loaded properties'
279 - GENE MAP:
280   - multiple views possible at the same time
281   - origin now at "12 o'clock"
282   - implemented 'jump to gene'
283 - tweaked file selection
284 - Enhanced Search Depth for Probe Match --> max 20 MM
285 - CLUSTALW:
286   - separated menus for fast and slow alignment
287   - most parameters accessible from inside ARB now
288 - upgraded to PHYLIP 3.6 (adds PROML)
289 - external programs may be called parallel (e.g. several treeing programs)
290 - fixed bugs in protml and integration of protml
291 - rewrote ASCII database import
292 - arb_repair for databases of any size (script for database repair)
293 - fixed bug in data compression
294 - increased internal cache size (alignments up to 400.000bp possible w/o performance collapse)
295 - ARBparsimony: increase hardcoded species limit (50.000 -> 250.000)
296 - GDE menus cleanup
297 - translation/re-alignment tweaked
298 - unalign right (EDIT4)
299 - visualization of SAIs in Probe Match Results
300 - changed formatting of probe match results; increase # of allowed matches to 100.000;
301   warn if results are truncated
302 - PT server for genes
303 - Probe design performance optimized
304 - fixed NEXUS export format
305 - exports group names into Newick format
306 - import XML tree files
307 - help for external tools now properly shown inside ARB
308
309Major changes in Beta 2003_08_22 (22 Aug 2003):
310
311 - automatic formatting of alignments
312 - SECEDIT may use EDIT4 colors
313 - fixed bootstrapping (DNAPARS, PROTPARS, PROTML(experimental!))
314 - updated clustalw to version 1.83
315 - Restore window sizes for ALL windows (too small sizes are ignored)
316 - new algorithm to add partial sequences to an existing tree
317 - PROT-parsimony was completely redesigned and works now most similar to DNA/RNA-parsimony
318 - Top area of ARB_NTREE may be reduced to maximize display area
319 - All arb menus may be detached (click dashed line at top of menu)
320 - visualization of SAIs (as background color behind Sequences)
321 - ARB_EDIT4 may save/use alignment-specific and alignment-type-specific properties
322 - PT-server occupies more memory => does less passes; more diagnostic output
323 - small changes to status window (unhide behavior/time estimation)
324 - menus and menu-hotkeys reorganized
325 - colored buttons in color config windows
326 - alignment concatenation (e.g. several different genes)
327 - merging data of similar species (according selected database field)
328 - keyboard commands for ARB_NTREE (mark/unmark/invert, collapse/expand)
329 - expanded sellists
330 - save/load fixed for multi probes
331 - Binary SAIs are editable in ARB_EDIT4
332 - Information windows are detachable (allows to have multiple windows showing different items)
333 - Scanning for hidden/unknown database fields improved and separated;
334   possibility to remove unused fields.
335 - new tabbed format in 'Export NDS' and 'Export matrix' (useful for star-calc/excel/etc.)
336 - updated fastDNAml to 1.2.2
337 - added AxML (accelerated fastDNAml 1.2.2)
338 - Field transfer definitions for exporting gene-species
339 - File Selection: - recursive search available
340 - The ARB_NTREE macro recording/execution has been fixed
341 - Colorize species (see demo.arb)
342 - Fixed missing-character-bug in Xfig, Print and Edit4-Info-Display
343 - 'IslandHopper' -- a new integrated aligner (beta)
344 - Many improvements and bugfixes to secondary structure editor:
345   - highlighting of search (i.e for probes) like in EDIT4
346   - interactive constraint editing (stretch/compress)
347   - probe info
348   - editing secondary structure in XFIG now possible
349   - visualization of SAIs
350 - import reads Unix, DOS, and MAC linefeeds
351 - NTREE/SAI/Etc/GnuPlot: calls gnuplot directly; more plotting features; basic help
352 - tree and sequence export to XML ( DTDs are provided in ./lib/dtd )
353   (reloading of these XML files is planned for the future)
354 - fixed problems with phylip-tree import/export (bootstrap values,comments,...)
355 - search in all database fields possible ('[all fields]')
356 - up to 10 quicksaves are kept
357 - new ACI functions: upper, lower, caps, eval
358 - variables for import filter programming
359 - extract gene-species: creates acc; extraction to existing alignments
360 - sequence of selected gene is mirrored in ARB_EDIT4/local_signature
361   (=> selected gene can be highlighted in primary editor)
362 - PCR primer-design for single genes
363 - when selecting a gene, the corresponding gene-species is selected (if found)
364 - save configuration for several windows (e.g. Search&Query, WWW, NDS, ...)
365 - file selection box in import window
366 - mark item with double click works in all search&query windows
367 - User masks: create new; 'edit enable' and 'marked' toggles (like in info window)
368 - Fixed command line help for all Arb-modules
369 - Fixed problem parsing fonts (should fix display problems with default fonts)
370 - Mark mode now works in list-view as well (ARB_NTREE)
371 - Fixed appearance of 'tiny little boxes' (everywhere)
372 - Redesign of ARB help:
373     - a HTML version is in $ARBHOME/lib/help_html
374     - a text version is in $ARBHOME/lib/help (like before, but now generated)
375
376Major changes in Beta 2001_11_07 (7 Nov 2001):
377
378 - design probes to maximum length of 60 nucleotides
379 - fastAligner1.03 bug fixed (chooses best match now in 'auto search' mode)
380 - import default changed to foreign data format, ali name '16s'
381 - printing of multi-page-trees works again
382 - implemented user defineable masks to access database fields
383 - fixed bugs in pt-server (lockup, unknown species just after building pt-server)
384 - improved performance during pt-server-build
385 - several programs coming along with ARB where updated (PHYLIP,...)
386 - reads EMBL genom files
387 - support for experiments (genom databases only)
388
389Major changes in Beta 2001_07_24 (24 Jul 2001):
390
391 - basic support for genoms (Gene Map, reads Genebank files)
392 - ported to libc6
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