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