1 ---------------------------------------------------------
2 Revision history for BioPerl core modules
3 ---------------------------------------------------------
4 The comprehensive history and ongoing development of BioPerl:
6 http://github.com/bioperl/bioperl-live
8 Some of that history is also highlighted on our wiki:
10 http://www.bioperl.org/wiki/Change_log
11 http://www.bioperl.org/wiki/History_of_BioPerl
13 Bugs and requested features list:
15 https://github.com/bioperl/bioperl-live/issues
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
23 * Bug/feature issue tracking has moved to GitHub Issues:
24 https://github.com/bioperl/bioperl-live/issues
28 * Bio::Search::HSP::GenericHSP
29 - Bug #3370, added a "posterior_string" method to retrieve the
30 posterior probability lines (PP) from HMMER3 reports [fjossandon]
31 - Added a "consensus_string" method to retrieve the consensus
32 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
33 * Bio::SearchIO::hmmer2
34 - The number of identical and conserved residues are now calculated
35 directly from the homology line [fjossandon]
36 - Now the Query Length and Hit Length are reported when the alignment
37 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
38 - Implemented the capture of the consensus structure lines [fjossandon]
39 * Bio::SearchIO::hmmer3
40 - The number of identical and conserved residues are now calculated
41 directly from the homology line [fjossandon]
42 - Now the Hit Length is reported when the alignment runs until the end
43 of the sequence/model ('.]' or '[]') [fjossandon]
44 - Implemented the capture of the consensus structure lines [fjossandon]
45 - Implemented the capture of the posterior probability lines [fjossandon]
46 - Completed the development of NHMMER parsing, including alignments [fjossandon]
47 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
48 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
49 "min_score", "min_bits, and "hit_filter" methods from
50 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
51 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
52 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
53 besides Blast, instead of being ignored. Added tests for all moved methods
54 using HMMER outputs and run the full test suite and everything pass [fjossandon]
55 * Bio::SeqIO::MultiFile
56 - Autodetection of file format [fangly]
57 * Bio::Tools::GuessSeqFormat:
58 - Format detection from non-seekable filehandles such as STDIN [fangly]
62 * Blast: Added support to changes in bl2seq from BLAST+ output, which
63 now uses "Subject=" instead of ">" to start hit lines [yschensandiego]
64 * Phylip: Return undef in "next_aln" at file end to avoid
65 an infinite loop [yschensandiego]
66 * HMMER3: When a hit description is too long, it is truncated in
67 the Scores table. In those cases, the more complete description from
68 the Annotation line (>>) will be used [fjossandon]
69 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
70 since it is now used by HMMER3 format in alignments [fjossandon]
71 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
72 to return undef if the query/hit length is unknown (like in some
73 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
74 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
75 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
76 added support to multi-query reports, reduced code redundancy,
77 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
78 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
79 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
80 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
81 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
82 * Double-quotes on paths are needed in some places [fjossandon]
83 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
84 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
85 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
86 with the latest changes made in their own repositories [fjossandon]
87 * General synching of files with the master branch [fjossandon]
88 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
89 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
90 * Fixed broken MeSH parser [fjossandon]
91 * Fixed missing detection of format in SeqIO when given a -string [fangly]
95 * Major Windows support updates! [fjossandon]
96 * MAKER update to allow for stricter standard codon table [cjfields]
97 * Better support for circular sequences [fjossandon]
98 * Fixes for some complex location types [fjossandon]
99 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
100 * Fix bug #2978 related to BLAST report type [fjossandon]
101 * Deobfuscator fixes [DaveMessina]
105 * Address CPAN test failures [cjfields]
106 * Add BIOPROJECT support for Genbank files [hyphaltip]
107 * Better regex support for HMMER3 output [bosborne]
111 * Minor update to address CPAN test failures
115 * Remove Bio::Biblio and related files [carandraug]
116 - this cause version clashes with an independently-released
117 version of Bio::Biblio
123 * Hash randomization fixes for perl 5.18.x
124 - Note: at least one module (Bio::Map::Physical) still has a failing test;
125 this is documented in bug #3446 and has been TODO'd; we will be pulling
126 Bio::Map and similar modules out of core into separate distributions in the
127 1.7.x release series [cjfields]
131 * Bio::Seq::SimulatedRead
132 - New module to represent reads taken from other sequences [fangly]
134 - Support of Clone::Fast as a faster cloning alternative [fangly]
136 - Moved the format() and variant() methods from Bio::*IO modules to
137 Bio::Root::IO [fangly]
138 - Can now use format() to get the type of IO format in use [fangly]
140 - New regexp() method to create regular expressions from IUPAC sequences
142 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
143 - Code refresh [fangly]
145 - Added support for the Greengenes and Silva taxonomies [fangly]
146 * Bio::Tree::TreeFunctionsI
147 - get_lineage_string() represents a lineage as a string [fangly]
148 - add_trait() returns instead of reporting an error when the column
149 number is exceeded in add_trait() [fangly]
150 - Option to support tree leaves without trait [fangly]
151 - Allow ID of 0 in trait files [fangly]
152 * Bio::DB::Taxonomy::list
153 - Misc optimizations [fangly]
154 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
155 * Bio::DB::Taxonomy::*
156 - get_num_taxa() returns the number of taxa in the database [fangly]
157 * Bio::DB::Fasta and Bio::DB::Qual
158 - support indexing an arbitrary list of files [fangly]
159 - user can supply an arbitrary index file name [fangly]
160 - new option to remove index file at the end [fangly]
162 - now handles IUPAC degenerate residues [fangly]
163 * Bio::PrimarySeq and Bio::PrimarySeqI
164 - speed improvements for large sequences [Ben Woodcroft, fangly]
166 - tightened and optimized quality string validation [fangly]
168 - new method and option 'block', to create FASTA output with space
169 intervaled blocks (similar to genbank or EMBL) has been implemented.
170 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
171 in favour of the methods 'width' and 'preferred_id_type` respectively.
173 - moved from bioperl-live into the separate distribution Bio-FeatureIO
174 * Bio::SeqFeature::Annotated
175 - moved from bioperl-live into the separate distribution Bio-FeatureIO
176 * Bio::Cluster::SequenceFamily
177 - improved performance when using get_members with overlapping multiple
179 * Bio::SearchIO::hmmer3
180 - now supports nhmmer [bosborne]
184 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
185 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
186 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
187 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
188 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
189 information was lost in a multi-result blast file [Paul Cantalupo]
190 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
191 total gaps [Paul Cantalupo]
192 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
193 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
194 when end of domain indicator is split across lines [Paul Cantalupo]
195 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
197 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
198 instances where blank lines are within sequences [cjfields]
199 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
201 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
202 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
204 * Various fixes for Stockholm file indexing and processing [bosborne]
205 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
206 breaks parsing [cjfields]
207 * Fix case where Bio::Seq::Meta* objects with no meta information could not
208 be reverse-complemented [fangly]
209 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
210 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
211 when unsure that values will be numerical [fangly]
212 * Fix undef warnings in Bio::SeqIO::embl [fangly]
213 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
214 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
215 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
217 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
218 source_tag and display_name must return a string, not undef [fangly]
219 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
220 add_SeqFeature takes a single argument [fangly]
221 * Use cross-platform filenames and temporary directory in
222 Bio::DB::Taxonomy::flatfile [fangly]
223 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
224 properly identified as existing taxa in the database [fangly]
225 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
226 without also passing a lineage to store [fangly]
227 * Prevent passing a directory to the gi2taxid option (-g) of
228 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
230 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
231 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
232 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
233 object before trying to access, and no longer returns repeated sequences.
240 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
241 modules using Ace will also be deprecated [lds, cjfields]
242 * Minor bug fix release
243 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
244 * Address Build.PL issues when DBI is not present [hartzell]
245 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
246 * Remove deprecated code for perl 5.14.0 compat [cjfields]
247 * Due to schema changes and lack of support for older versions, support
248 for NeXML 0.9 is only (very) partially implemented.
249 See: https://redmine.open-bio.org/issues/3207
253 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
254 docs [genehack, cjfields]
255 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
256 module version from dist_version (probably not the best way to do this,
257 but it seems to work) [rbuels, cjfields]
260 1.6.900 April 14, 201
264 * This will probably be the last release to add significant features to
265 core modules; subsequent releases will be for bug fixes alone.
266 We are planning on a restructuring of core for summer 2011, potentially
267 as part of the Google Summer of Code. This may become BioPerl 2.0.
268 * Version bump represents 'just prior to v 1.7'. We may have point
269 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
270 This code essentially is what is on the github master branch.
274 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
276 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
277 - removal of Scalar::Util::weaken code, which was causing odd headaches
278 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
279 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
281 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
284 - bug 2515 - new contribution [Ryan Golhar, jhannah]
286 - support for reading Maq, Sam and Bowtie files [maj]
287 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
288 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
289 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
290 - bug 2726: reading/writing granularity: whole scaffold or one contig
291 at a time [Joshua Udall, fangly]
293 - Added parsing of xrefs to OBO files, which are stored as secondary
294 dbxrefs of the cvterm [Naama Menda]
295 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
296 * PAML code updated to work with PAML 4.4d [DaveMessina]
300 * [3198] - sort tabular BLAST hits by score [DaveMessina]
301 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
302 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
303 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
305 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
306 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
307 * [3164] - TreeFunctionsI syntax bug [gjuggler]
308 * [3163] - AssemblyIO speedup [fangly]
309 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
311 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
312 * [3158] - fix EMBL file mis-parsing [cjfields]
313 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
315 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
316 * [3148] - URL change for UniProt [cjfields]
317 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
318 * [3136] - HMMer3 parser fixes [kblin]
319 * [3126] - catch description [Toshihiko Akiba]
320 * [3122] - Catch instances where non-seekable filehandles were being
321 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
322 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
323 [dukeleto, rbuels, cjfields]
324 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
326 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
327 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
329 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
330 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
331 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
332 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
333 * [3086] - EMBL misparsing long tags [kblin, cjfields]
334 * [3085] - CommandExts and array of files [maj, hyphaltip]
335 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
336 for alignment slices [Ha X. Dang, cjfields]
337 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
338 * [3073] - fix parsing of GenBank files from RDP [cjfields]
339 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
340 * [3064] - All-gap midline BLAST report issues [cjfields]
341 * [3063] - BLASt report RID [Razi Khaja, cjfields]
342 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
343 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
344 * [3039] - correct Newick output root node branch length [gjuggler,
346 * [3038] - SELEX alignment error [Bernd, cjfields]
347 * [3033] - PrimarySeq ID setting [Bernd, maj]
348 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
349 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
350 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
351 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
352 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
353 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
354 PAML 4.4d [DaveMessina]
355 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
357 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
358 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
359 * [3017] - using threads with Bio::DB::GenBank [cjfields]
360 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
361 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
362 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
363 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
364 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
366 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
367 * [2977] - TreeIO issues [DaveMessina]
368 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
369 * [2944] - Bio::Tools::GFF score [cjfields]
370 * [2942] - correct MapTiling output [maj]
371 * [2939] - PDB residue insertion codes [John May, maj]
372 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
373 * [2928] - GuessSeqFormat raw [maj]
374 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
375 * [2922] - open() directive issue [cjfields]
376 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
377 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
378 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
379 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
381 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
382 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
383 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
384 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
385 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
386 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
387 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
388 * [2758] - Bio::AssemblyIO ace problems [fangly]
389 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
390 * [2726] - ace file IO [Josh, fangly]
391 * [2700] - Refactor Build.PL [cjfields]
392 * [2673] - addition of simple Root-based clone() method [cjfields]
393 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
394 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
395 * [2594] - Bio::Species memory leak [cjfields]
396 * [2515] - GenBank XML parser [jhannah]
397 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
398 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
399 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
401 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
405 * Bio::Expression modules - these were originally designed to go with the
406 bioperl-microarray suite of tools, however they have never been completed
407 and so have been removed from the distribution. The original code has
408 been moved into the inactive bioperl-microarray suite. [cjfields]
412 * Repository moved from Subversion (SVN) to
413 http://github.com/bioperl/bioperl-live [cjfields]
414 * Bug database has moved to Redmine (https://redmine.open-bio.org)
415 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
416 Thieme have been moved to their own distribution (Bio-Microarray).
419 1.6.1 Sept. 29, 2009 (point release)
420 * No change from last alpha except VERSION and doc updates [cjfields]
422 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
423 * Fix for silent OBDA bug related to FASTA validation [cjfields]
425 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
426 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
427 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
429 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
431 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
432 * WinXP test fixes [cjfields, maj]
433 * BioPerl.pod added for descriptive information, fixes CPAN indexing
435 * Minor doc fixes [cjfields]
437 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
438 * Fix tests failing due to merging issues [cjfields]
439 * More documentation updates for POD parsing [cjfields]
441 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
443 - fix YAML meta data generation [cjfields]
445 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
446 * Bio::Align::DNAStatistics
447 - fix divide by zero problem [jason]
449 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
450 * Bio::AlignIO::stockholm
451 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
452 * Bio::Assembly::Tools::ContigSpectrum
453 - function to score contig spectrum [fangly]
454 * Bio::DB::EUtilities
455 - small updates [cjfields]
457 - berkeleydb database now autoindexes wig files and locks correctly
460 - various small updates for stability; tracking changes to LANL
461 database interface [maj]
462 * Bio::DB::SeqFeature (lots of updates and changes)
463 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
464 - bug 2835 - patch [Dan Bolser]
465 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
467 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
468 * Bio::Factory::FTLocationFactory
469 - mailing list bug fix [cjfields]
471 - performance work on column_from_residue_number [hartzell]
472 * Bio::Matrix::IO::phylip
473 - bug 2800 - patch to fix phylip parsing [Wei Zou]
475 - Google Summer of Code project from Chase Miller - parsers for Nexml
476 file format [maj, chmille4]
478 - Make Individual, Population, Marker objects AnnotatableI [maj]
479 - simplify LD code [jason]
481 - deal with empty intersection [jason]
483 - significant overhaul of Bio::Restriction system: complete support for
484 external and non-palindromic cutters. [maj]
486 - CPANPLUS support, no automatic installation [sendu]
488 - allow IO::String (regression fix) [cjfields]
489 - catch unintentional undef values [cjfields]
490 - throw if non-fh is passed to -fh [maj]
491 * Bio::Root::Root/RootI
492 - small debugging and core fixes [cjfields]
494 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
495 * Bio::Root::Utilities
496 - bug 2737 - better warnings [cjfields]
498 - tiling completely refactored, HOWTO added [maj]
499 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
500 will deprecate usage of the older tiling code in the next BioPerl
502 - small fixes [cjfields]
504 - Infernal 1.0 output now parsed [cjfields]
505 - new parser for gmap -f9 output [hartzell]
506 - bug 2852 - fix infinite loop in some output [cjfields]
507 - blastxml output now passes all TODO tests [cjfields]
508 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
509 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
510 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
511 * Bio::Seq::LargePrimarySeq
512 - delete tempdirs [cjfields]
513 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
515 - extract regions based on quality threshold value [Dan Bolser, heikki]
516 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
517 * Bio::SeqFeature::Lite
518 - various Bio::DB::SeqFeature-related fixes [lstein]
519 * Bio::SeqFeature::Tools::TypeMapper
520 - additional terms for GenBank to SO map [scain]
521 * Bio::SeqIO::chadoxml
522 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
524 - support for CDS records [dave_messina, Sylvia]
526 - complete refactoring to handle all FASTQ variants, perform validation,
527 write output. API now conforms with other Bio* parsers and the rest of
528 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
530 * Bio::SeqIO::genbank
531 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
532 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
533 * Bio::SeqIO::largefasta
534 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
536 - add option for 'single' and 'multiple'
538 - bug 2881 - fix scf round-tripping [Adam Søgren]
540 - bug 2766, 2810 - copy over tags from features, doc fixes [David
543 - bug 2793 - patch for add_seq index issue [jhannah, maj]
544 - bug 2801 - throw if args are required [cjfields]
545 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
546 [Tristan Lefebure, maj]
547 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
548 - fix POD and add get_SeqFeatures filter [maj]
549 * Bio::Tools::dpAlign
550 - add support for LocatableSeq [ymc]
551 - to be moved to a separate distribution [cjfields, rbuels]
552 * Bio::Tools::EUtilities
553 - fix for two bugs from mail list [Adam Whitney, cjfields]
554 - add generic ItemContainerI interface for containing same methods
557 - fix up code, add more warnings [cjfields]
558 - to be moved to a separate distribution [cjfields, rbuels]
559 * Bio::Tools::Primer3
560 - bug 2862 - fenceposting issue fixed [maj]
561 * Bio::Tools::Run::RemoteBlast
562 - tests for remote RPS-BLAST [mcook]
563 * Bio::Tools::SeqPattern
564 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
565 * Bio::Tools::tRNAscanSE
566 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
568 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
569 * Bio::Tree::Statistics
570 - several methods for calculating Fitch-based score, internal trait
571 values, statratio(), sum of leaf distances [heikki]
573 - bug 2869 - add docs indicating edge case where nodes can be
574 prematurely garbage-collected [cjfields]
575 - add as_text() function to create Tree as a string in specified format
577 * Bio::Tree::TreeFunctionsI
578 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
580 * Bio::TreeIO::newick
581 - fix small semicolon issue [cjfields]
583 - update to bp_seqfeature_load for SQLite [lstein]
584 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
585 - fastam9_to_table - fix for MPI output [jason]
586 - gccalc - total stats [jason]
588 - POD cleanup re: FEEDBACK section [maj, cjfields]
589 - cleanup or fix dead links [cjfields]
590 - Use of no_* methods (indicating 'number of something') is deprecated
591 in favor of num_* [cjfields]
592 - lots of new tests for the above bugs and refactors [everyone!]
593 - new template for Komodo text editor [cjfields]
596 * Feature/Annotation rollback
597 - Problematic changes introduced prior to the 1.5 release have been
598 rolled back. These changes led to subtle bugs involving operator
599 overloading and interface methods.
600 - Behavior is very similar to that for BioPerl 1.4, with tag values
601 being stored generically as simple scalars. Results in a modest
604 - Split into a separate distribution on CPAN, primarily so development
605 isn't reliant on a complete BioPerl release.
606 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
607 is only available via Subversion (via bioperl-live main trunk)
609 - Common test bed for all BioPerl modules
611 - Common Module::Build-based subclass for all BioPerl modules
612 * Bio::DB::EUtilities
613 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
614 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
615 and user agent request posting and retrieval
616 * Test implementation and reorganization
617 - Tests have been reorganized into groups based on classes or use
619 - Automated test coverage is now online:
620 http://www.bioperl.org/wiki/Test_Coverage
621 - After this release, untested modules will be moved into a
622 separate developer distribution until tests can be derived.
623 Also, new modules to be added are expected to have a test suite
624 and adequate test coverage.
626 1.5.2 Developer release
628 Full details of changes since 1.5.1 are available online at:
629 http://www.bioperl.org/wiki/Change_log
630 The following represents a brief overview of the most important changes.
633 - Overhaul. Brand new system fully allows markers to have multiple
634 positions on multiple maps, and to have relative positions. Should be
638 - This module and all the modules in the Taxonomy directory now
639 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
644 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
646 * New methods ancestor(), each_Descendent() and _handle_internal_id().
648 * Allows for different database modules to create Bio::Taxon objects
649 with the same internal id when the same taxon is requested from each.
652 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
654 * No longer includes the fake root node 'root'; there are multiple roots
655 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
658 * get_node() has new option -full
660 * Caches data retrieved from website
663 - Now a Bio::Taxon. Carries out the species name -> specific name munging
664 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
665 backward compatability in species() method.
667 o Bio::Search and Bio::SearchIO
668 - Overhaul. The existing system has been sped up via some minor changes
669 (mostly gain-of-function to the API). Bio::PullParserI is introduced
670 as a potential eventual replacment for the existing system, though as
671 yet only a Hmmpfam parser exists written using it.
674 1.5.1 Developer release
676 o Major problem with how Annotations were written out with
677 Bio::Seq is fixed by reverting to old behavior for
678 Bio::Annotation objects.
683 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
684 expect at l east 9 spaces at the beginning of a line to
685 indicate line wrapping.
687 * Treat multi-line SOURCE sections correctly, this defect broke
688 both common_name() and classification()
690 * parse swissprot fields in genpept file
692 * parse WGS genbank records
695 * Changed regexp for ID line. The capturing parentheses are
696 the same, the difference is an optional repeated-not-semi-
697 colon expression following the captured \S+. This means the
698 regexp works when the division looks like /PRO;/ or when the
699 division looks like /ANG ;/ - the latter is from EMBL
702 * fix ID line parsing: the molecule string can have spaces in
703 it. Like: "genomic DNA"
705 - swiss.pm: bugs #1727, #1734
708 * Added parser for entrezgene ASN1 (text format) files.
709 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
713 - maf.pm coordinate problem fixed
715 o Bio::Taxonomy and Bio::DB::Taxonomy
717 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
718 can be done via Web without downloading all the sequence.
720 o Bio::Tools::Run::RemoteBlast supports more options and complies
721 to changes to the NCBI interface. It is reccomended that you
722 retrieve the data in XML instead of plain-text BLAST report to
723 insure proper parsing and retrieval of all information as NCBI
724 fully expects to change things in the future.
726 o Bio::Tree and Bio::TreeIO
728 - Fixes so that re-rooting a tree works properly
730 - Writing out nhx format from a newick/nexus file will properly output
731 bootstrap information. The use must move the internal node labels over
733 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
734 $node->bootstrap($node->id);
737 - Nexus parsing is much more flexible now, does not care about
740 - Cladogram drawing module in Bio::Tree::Draw
742 - Node height and depth now properly calculated
744 - fix tree pruning algorithm so that node with 1 child gets merged
746 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
747 bugs and improvements were added, see Gbrowse mailing list for most of
750 o Bio::DB::GFF partially supports GFF3. See information about
751 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
753 o Better location parsing in Bio::Factory::FTLocationFactory -
754 this is part of the engine for parsing EMBL/GenBank feature table
755 locations. Nested join/order-by/complement are allowed now
757 o Bio::PrimarySeqI->translate now takes named parameters
759 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
760 reconstruction) is now supported. Parsing different models and
761 branch specific parametes are now supported.
763 o Bio::Factory::FTLocationFactory - parse hierarchical locations
766 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
767 for getter/setter functions
771 - blast bug #1739; match scientific notation in score
772 and possible e+ values
774 - blast.pm reads more WU-BLAST parameters and parameters, match
775 a full database pathname,
777 - Handle NCBI WEB and newer BLAST formats specifically
778 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
780 - psl off-by-one error fixed
782 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
783 and HSPs can be constructed from them.
785 - HSPs query/hit now have a seqdesc field filled out (this was
786 always available via $hit->description and
787 $result->query_description
789 - hmmer.pm can parse -A0 hmmpfam files
791 - Writer::GbrowseGFF more customizeable.
793 o Bio::Tools::Hmmpfam
794 make e-value default score displayed in gff, rather than raw score
795 allow parse of multiple records
798 1.5 Developer release
800 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
801 provide Jukes-Cantor and Kimura pairwise distance methods,
804 o Bio::AlignIO support for "po" format of POA, and "maf";
805 Bio::AlignIO::largemultifasta is a new alternative to
806 Bio::AlignIO::fasta for temporary file-based manipulation of
807 particularly large multiple sequence alignments.
809 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
810 be treated similarly as an assembled contig.
812 o Bio::CodonUsage provides new rare_codon() and probable_codons()
813 methods for identifying particular codons that encode a given
816 o Bio::Coordinate::Utils provides new from_align() method to build
817 a Bio::Coordinate pair directly from a
818 Bio::Align::AlignI-conforming object.
820 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
821 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
822 web service using standard Pubmed query syntax, and retrieve
825 o Bio::DB::GFF has various sundry bug fixes.
827 o Bio::FeatureIO is a new SeqIO-style subsystem for
828 writing/reading genomic features to/from files. I/O classes
829 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
830 classes only read/write Bio::SeqFeature::Annotated objects.
831 Notably, the GFF v3 class requires features to be typed into the
834 o Bio::Graph namespace contains new modules for manipulation and
835 analysis of protein interaction graphs.
837 o Bio::Graphics has many bug fixes and shiny new glyphs.
839 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
840 indexing for HMMER reports and FASTA qual files, respectively.
842 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
843 new objects that can be placed within a Bio::Map::MapI-compliant
844 genetic/physical map; Bio::Map::Physical provides a new physical
845 map type; Bio::MapIO::fpc provides finger-printed clone mapping
848 o Bio::Matrix::PSM provide new support for postion-specific
849 (scoring) matrices (e.g. profiles, or "possums").
851 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
852 be instantiated without explicitly using Bio::OntologyIO. This
853 is possible through changes to Bio::Ontology::OntologyStore to
854 download ontology files from the web as necessary. Locations of
855 ontology files are hard-coded into
856 Bio::Ontology::DocumentRegistry.
858 o Bio::PopGen includes many new methods and data types for
859 population genetics analyses.
861 o New constructor to Bio::Range, unions(). Given a list of
862 ranges, returns another list of "flattened" ranges --
863 overlapping ranges are merged into a single range with the
864 mininum and maximum coordinates of the entire overlapping group.
866 o Bio::Root::IO now supports -url, in addition to -file and -fh.
867 The new -url argument allows one to specify the network address
868 of a file for input. -url currently only works for GET
869 requests, and thus is read-only.
871 o Bio::SearchIO::hmmer now returns individual Hit objects for each
872 domain alignment (thus containing only one HSP); previously
873 separate alignments would be merged into one hit if the domain
874 involved in the alignments was the same, but this only worked
875 when the repeated domain occured without interruption by any
876 other domain, leading to a confusing mixture of Hit and HSP
879 o Bio::Search::Result::ResultI-compliant report objects now
880 implement the "get_statistics" method to access
881 Bio::Search::StatisticsI objects that encapsulate any
882 statistical parameters associated with the search (e.g. Karlin's
883 lambda for BLAST/FASTA).
885 o Bio::Seq::LargeLocatableSeq combines the functionality already
886 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
888 o Bio::SeqFeature::Annotated is a replacement for
889 Bio::SeqFeature::Generic. It breaks compliance with the
890 Bio::SeqFeatureI interface because the author was sick of
891 dealing with untyped annotation tags. All
892 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
893 compliant, and accessible through Bio::Annotation::Collection.
895 o Bio::SeqFeature::Primer implements a Tm() method for primer
896 melting point predictions.
898 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
899 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
901 o Bio::Taxonomy::Node now implements the methods necessary for
902 Bio::Species interoperability.
904 o Bio::Tools::CodonTable has new reverse_translate_all() and
905 make_iupac_string() methods.
907 o Bio::Tools::dpAlign now provides sequence profile alignments.
909 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
911 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
914 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
915 for designing small inhibitory RNA.
917 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
918 methods based on a distance matrix.
920 o Bio::Tree::Statistics provides an assess_bootstrap() method to
921 calculate bootstrap support values on a guide tree topology,
922 based on provided bootstrap tree topologies.
924 o Bio::TreeIO now supports the Pagel (PAG) tree format.
930 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
932 o Bio::Graphics will work with gd1 or gd2
935 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
937 - blast.pm Parse multi-line query fields properly
938 - small speed improvements to blasttable.pm and others
940 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
941 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
942 supporting more complex queries
945 1.4. Stable major release
947 Since initial 1.2.0, 3000 separate changes have been made to make this release.
949 o installable scripts
951 o global module version from Bio::Root:Version
954 - major improvements; SVG support
957 - population genetics
958 - support several population genetics types of questions.
959 - Tests for statistical neutrality of mutations
960 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
961 Tests of population structure (Wright's F-statistic: Fst) is in
962 Bio::PopGen::PopStats. Calculating composite linkage
963 disequilibrium (LD) is available in Bio::PopGen::Statistics as
965 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
966 and csv (comma delimited formatted) data.
968 - a directory for implementing population simulations has
969 been added Bio::PopGen::Simulation and 2 simulations - a
970 Coalescent and a simple single-locus multi-allele genetic drift
971 simulation have been provided. This replaces the code in
972 Bio::Tree::RandomTree which has been deprecated until proper
973 methods for generating random phylogenetic trees are
977 - new restrion analysis modules
979 o Bio::Tools::Analysis
980 - web based DNA and Protein analysis framework and several
984 - per residue annotable sequences
987 - Bio::Matrix::PSM - Position Scoring Matrix
988 - Bio::Matrix::IO has been added for generalized parsing of
989 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
990 initial implementations for parsing BLOSUM/PAM and Phylip
991 Distance matricies respectively. A generic matrix
992 implementation for general use was added in
993 Bio::Matrix::Generic.
1000 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
1001 - small inhibitory RNA
1003 o Bio::SeqFeature::Tools
1004 - seqFeature mapping tools
1005 - Bio::SeqFeature::Tools::Unflattener.pm
1006 -- deal with mapping GenBank feature collections into
1007 Chado/GFF3 processable feature sets (with SO term mappings)
1009 o Bio::Tools::dpAlign
1010 - pure perl dynamic programming sequence alignment
1013 o new Bio::SearchIO formats
1014 - axt and psl: UCSC formats.
1015 - blasttable: NCBI -m 8 or -m 9 format from blastall
1017 o new Bio::SeqIO formats
1018 - chado, tab, kegg, tigr, game
1019 - important fixes for old modules
1023 o improved Bio::Tools::Genewise
1025 o Bio::SeqIO now can recongnize sequence formats automatically from
1028 o new parsers in Bio::Tools:
1029 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1031 o Bio::DB::Registry bugs fixed
1032 - BerkeleyDB-indexed flat files can be used by the OBDA system
1033 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1034 used by the OBDA system
1036 o several new HOWTOs
1037 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1040 o hundreds of new and improved files
1044 o Bio::Tree::AlleleNode has been updated to be a container of
1045 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1050 1.2.3 Stable release update
1051 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1053 o Bug #1477 - Sel --> Sec abbreviation fixed
1054 o Fix bug #1487 where paring in-between locations when
1055 end < start caused the FTLocationFactory logic to fail.
1056 o Fix bug #1489 which was not dealing with keywords as an
1057 arrayref properly (this is fixed on the main trunk because
1058 keywords returns a string and the array is accessible via
1060 o Bio::Tree::Tree memory leak (bug #1480) fixed
1061 Added a new initialization option -nodelete which
1062 won't try and cleanup the containing nodes if this
1064 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1065 this was only present on the branch for the 1.2.1 and 1.2.2 series
1066 - Also merged main trunk changes to the branch which make
1067 newick -> nhx round tripping more effective (storing branch length
1068 and bootstrap values in same locate for NodeNHX and Node
1069 implementations.) Fixes to TreeIO parsing for labeled internal
1070 also required small changes to TreeIO::nhx. Improved
1071 tests for this module as well.
1073 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1074 gapped blast properly (was losing hit significance values due to
1075 the extra unexpeted column).
1076 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1077 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1078 although doesn't try to correct it - will get the negative
1079 number for you. Added a test for this as well.
1080 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1081 has no top-level family classification scores but does have scores and
1082 alignments for individual domains.
1083 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1084 regular expression to match the line was missing the possibility of
1085 an extra space. This is rare, which is why we probably did not
1087 - BLAST parsing picks up more of the statistics/parameter fields
1088 at the bottom of reports. Still not fully complete.
1089 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1090 were fixed to include many improvements and added flexiblity
1091 in outputting the files. Bug #1495 was also fixed in the process.
1093 - Update for GFF3 compatibility.
1094 - Added scripts for importing from UCSC and GenBank.
1095 - Added a 1.2003 version number.
1098 - Added a 1.2003 version number.
1099 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1100 properly writing keywords out.
1101 o Bio::SeqIO::genbank
1102 - Fixed bug/enhancement #1513 where dates of
1103 the form D-MMM-YYYY were not parsed. Even though this is
1104 invalid format we can handle it - and also cleanup the date
1105 string so it is properly formatted.
1106 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1107 and written with Genbank format. Similarly bug #1515 is fixed to
1108 parse in the ORIGIN text.
1109 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1110 to specify the ID type, one of (accession accession.version
1111 display primary). See Bio::SeqIO::preferred_id_type method
1112 documentation for more information.
1113 o Unigene parsing updated to handle file format changes by NCBI
1115 1.2.2 Stable release update
1117 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1118 - auto-discover ontology name
1119 - bug in parsing relationships when certain characters are in the term
1120 - fixed hard-coded prefix for term identifiers
1121 - various smaller issues
1123 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1124 of Bio::Ontology::TermI
1126 o brought the OBDA Registry code up to latest specs
1130 - accession number retrieval fixed
1132 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1134 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1135 #1459 which now properly report alignment start/end info
1136 for translated BLAST/FASTA searches.
1138 o Bio::TreeIO::newick can parse labeled internal nodes
1140 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1141 for BLASTX if if you provide -report_type => 'BLASTX' when
1142 initializing a BPbl2seq object. Bioperl 1.3 will have better
1143 support for bl2seq in the SearchIO system.
1145 o Bio::Root::IO support a -noclose boolean flag which will not
1146 close a filehandle upon object cleanup - useful when sharing
1147 a filehandle among objects. Additionally code added s.t.
1148 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1150 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1152 o Bio::SeqIO::genbank
1153 - bug #1456 fixed which generated extra sequence lines
1154 - write moltype correctly for genpept
1156 1.2.1 Stable release update
1158 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1160 o Addition from main trunk of Ontology objects, principly to allow
1161 BioSQL releases against 1.2.1
1163 o Fixes and cleanup of Bio::Coordinate modules
1165 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1166 the primary accession number
1168 o Other bug fixes, including bpindex GenBank fix
1170 o Bio::SeqIO::genbank bug #1389 fixed
1172 1.2 Stable major release
1174 o More functionality added to Bio::Perl, the newbie module
1176 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1177 Support for New Hampshire Extended (NHX) format parsing.
1179 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1180 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1183 o New ontology parsing Bio::Ontology
1185 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1186 multi-report (mlib) fasta reports, support for waba and exonerate.
1188 o Bio::ClusterIO for parsing Unigene clusters
1190 o Bio::Assembly added for representing phrap and ace assembly clusters.
1192 o Rudimentary support for writing Chado XML (see
1193 GMOD project: www.gmod.org for more information)
1195 o Bio::Coordinate for mapping between different coordinate systems such
1196 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1197 features into different coordinate systems.
1199 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1200 with the get_Stream_by_query method and supports the latest
1201 NCBI eutils interface.
1203 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1204 object for extracting subsets of features : currently only
1205 supports extraction by location.
1207 1.1.1 Developer release
1209 o Deprecated modules are now listed in the DEPRECATED file
1211 o New HowTo documents located in doc/howto describing
1212 a domain of Bioperl.
1214 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1215 and all old bugs are searchable through the bugzilla interface.
1217 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1218 have been addressed.
1220 o Support for Genewise parsing in Bio::Tools::Genewise
1222 o Start of Ontology framework with Bio::Ontology
1224 o Speedup to the Bio::Root::Root object method _rearrange.
1225 A global _load_module method was implemented to simplify the
1226 dynamic loading of modules ala Bio::SeqIO::genbank. This
1227 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1230 o Several performance improvements to sequence parsing in Bio::SeqIO.
1231 Attempt to speedup by reducing object creation overhead.
1233 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1234 method for sequence retrieval with their E-utils CGI scripts.
1235 More work to support Entrez queries to their fullest is planned
1238 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1240 1.1 Developer release
1242 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1243 this separation removes some of the complexity in our test suite
1244 and separates the core modules in bioperl from those that need
1245 external programs to run.
1247 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1248 not run into trouble running the makefile
1250 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1251 read,create,and write locations for grouped/split locations
1252 (like mRNA features on genomic sequence).
1254 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1255 and PAML (codeml,aaml, etc) parsing.
1257 o Bio::Tree:: objects expanded to handle testing monophyly,
1258 paraphyly, least common ancestor, etc.
1260 o Bio::Coordinate for mapping locations from different coordinate spaces
1262 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1263 added for parsing hmmpfam and hmmsearch output.
1265 o Bio::SearchIO::Writer::TextResultWriter for outputting
1266 a pseudo-blast textfile format
1269 1.0.2 Bug fix release
1271 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1272 in this release will not work after December 2002 when NCBI
1273 shuts off the old Entrez cgi scripts. We have already fixed
1274 on our main development branch and the functionality will be
1275 available in the next stable bioperl release (1.2) slated for
1278 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1279 testset by Robin Emig. These were fixed as was the get_aln
1280 method in Bio::Search::HSP::GenericHSP to handle the extra
1281 context sequence that is provided with a FastA alignment.
1283 o Migrating differences between Bio::Search::XX::BlastXX to
1284 Bio::Search::XX::GenericXX objects. This included mechanism
1285 to retrieve whole list of HSPs from Hits and whole list of Hits from
1286 Results in addition to the current next_XX iterator methods that
1287 are available. Added seq_inds() method to GenericHSP which identifies
1288 indexes in the query or hit sequences where conserved,identical,gaps,
1289 or mismatch residues are located (adapted from Steve Chervitz's
1290 implementation in BlastHSP).
1292 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1293 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1295 o Bio::Graphics glyph set improved and extended for GBrowse release
1297 o Bio::Tree::Tree get_nodes implementation improvement thanks
1298 to Howard Ross notice performance problem when writing out
1301 o Bio::Location::Fuzzy::new named parameter -loc_type became
1302 -location_type, Bio::Location::Simple::new named parameter
1303 -seqid becamse -seq_id.
1305 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1306 was mis-detecting that gaps should be placed at the beginning of
1307 the alignment when the best alignment starts internally in the
1310 1.0.1 Bug fix release
1312 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1314 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1315 and mixed (3.3 - 3.4) versions of FASTA.
1317 o Small API change to add methods for completeness across
1318 implementations of Bio::Search objects. These new methods
1319 in the interface are implemented by the GenericXX object as well
1320 as the BlastXX objects.
1321 * Bio::Search::Result::ResultI
1322 - hits() method returns list of all Hits (next_hit is an
1325 * Bio::Search::Hit::HitI
1326 - hsps() method returns list of all HSPs (next_hsp is an
1329 o The Bio::SearchIO::Writer classes have been fixed to handle results
1330 created from either psiblast (Search::BlastXX objects) or
1331 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1332 has to be done here to make it work properly and will nee major
1335 o Bugs in Bio::Tools::HMMER fixed, including
1336 * #1178 - Root::IO destructor wasn't being called
1337 * #1034 - filter_on_cutoff now behaves properly
1339 o Bio::SeqFeature::Computation initialization args fixed and
1342 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1344 o Updated FAQ with more example based answers to typical questions
1346 o Bug #1202 was fixed which would improperly join together qual values
1347 parsed by Bio::SeqIO::qual when a trailing space was not present before
1350 1.0.0 Major Stable Release
1352 This represents a major release of bioperl with significant
1353 improvements over the 0.7.x series of releases.
1355 o Bio::Tools::Blast is officially deprecated. Please see
1356 Bio::SearchIO for BLAST and FastA parsing.
1358 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1359 Bio::LocationI objects as well as start/end.
1361 o Bio::Biblio contains modules for Bibliographic data.
1362 Bio::DB::Biblio contains the query modules. Additionally one can
1363 parse medlinexml from the ebi bibliographic query service (BQS)
1364 system and Pubmed xml from NCBI. See Martin Senger's
1365 documentation in Bio::Biblio for more information.
1367 o Bio::DB::Registry is a sequence database registry part of
1368 Open Bioinformatics Database Access. See
1369 http://obda.open-bio.org for more information.
1371 o File-based and In-Memory Sequence caching is provided by
1372 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1375 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1376 been added by Lincoln Stein.
1378 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1380 o A FAQ has been started and is included in the release to provide
1381 a starting point for frequent questions and issues.
1383 0.9.3 Developer's release
1385 o Event based parsing system improved (SearchIO). With parsers for
1386 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1387 Additionally a lazy parsing system for text and html blast reports was
1388 added and is called psiblast (name subject to change in future releases).
1390 o Bio::Search objects improved and standardized with associated Interfaces
1391 written. The concept of a search "Hit" was standardized to be called
1392 "hit" consistently and the use of "subject" was deprecated in all active
1395 o Bio::Structure added (since 0.9.1) for Protein structure objects
1396 and PDB parser to retrieve and write these structures from data files.
1398 o Several important Bio::DB::GFF bug fixes for handling features that
1399 are mapped to multiple reference points. Updated mysql adaptor
1400 so as to be able to store large (>100 megabase) chunks of DNA into
1401 Bio::DB::GFF databases.
1403 0.9.2 Developer's release
1405 o Bio::Search and Bio::SearchIO system introduced for event based
1406 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1407 in text and XML and FASTA reports in standard output format.
1409 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1410 generator is included in Bio::TreeIO::RandomTrees and a
1411 statistics module for evaluating.
1413 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1414 server for DAS servers.
1416 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1417 files. The entire BPlite system migrated to using Bio::Root::IO
1418 for the data stream.
1420 o Bio::Tools::Alignment for Consed and sequence Trimming
1423 o Bio::Structure for Protein structure information and parsing
1425 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1426 cgi-bin entry point which should be more reliable.
1428 o Bio::Map and Bio::MapIO for biological map navigation and a
1429 framework afor parsing them in. Only preliminary work here.
1431 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1432 Future work will integrate Pise and allow submission of analysis on
1435 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1436 introduced as new objects for handling Sequence Annotation
1437 information (dblinks, references, etc) and is more robust that
1440 o Bio::Tools::FASTAParser introduced.
1442 o Scripts from the bioperl script submission project and new
1443 scripts from bioperl authors are included in "scripts" directory.
1445 o Factory objects and interfaces are being introduced and are more
1448 o Bio::Root::Root introduced as the base object while
1449 Bio::Root::RootI is now simply an interface.
1451 o Bio::DB::RefSeq provides database access to copy of the NCBI
1452 RefSeq database using the EBI dbfetch script.
1454 0.9.0 Developer's release
1456 o perl version at least 5.005 is now required instead of perl 5.004
1458 o Bio::Tools::Run::RemoteBlast is available for running remote
1461 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1463 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1464 Also added are related modules UTR3, UTR5, Exon, Intron,
1465 Promotor, PolyA and Transcript.
1467 o Speedup of translate method in PrimarySeq
1469 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1470 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1472 o Various fixes to Variation toolkit
1474 o Bio::DB::EMBL provides database access to EMBL sequence data.
1475 Bio::DB::Universal provides a central way to point to indexes
1476 and dbs in a single interface.
1478 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1480 o Bio::Factory::EMBOSS is still in design phase as is
1481 Bio::Factory::ApplicationFactoryI
1483 o Dia models for bioperl design are provided in the models/ directory
1485 0.7.2 Bug fix release
1487 o documentation fixes in many modules - SYNOPSIS code verified
1488 to be runnable in many (but not all modules)
1490 o corrected MANIFEST file from 0.7.1 release
1492 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1495 o Bio::SeqIO::genbank
1496 * Correct parsing and writing of genbank format with protein data
1497 * moltype and molecule separation
1499 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1501 o Bio::SimpleAlign fixed to correctly handle consensus
1502 sequence calculation
1504 o Bio::Tools::HMMER supports hmmer 2.2g
1506 o Bio::Tools::BPlite to support report type specific parsing. Most
1507 major changes are not on the 0.7 branch.
1509 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1512 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1513 in several types of mutations:
1514 1.) AA level: deletion, complex
1515 2.) AA level: complex, inframe
1516 3.) RNA level: silent
1518 o BPbl2seq parsing of empty reports will not die, but will return
1519 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1520 $report->query() and $report->subject() methods. So an easy
1521 way to test if report was empty is to see if
1522 $report->query->seqname is undefined.
1524 0.7.1 Bug fix release
1526 o Better parsing of genbank/EMBL files especially fixing bugs
1527 related to Feature table parsing and locations on remote
1528 sequences. Additionally, species name parsing was better.
1530 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1531 which include a number of header lines.
1533 o More strict genbank and EMBL format writing (corrected number of
1534 spaces where appropriate).
1536 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1537 for related BPlite BUGS that are unresolved in this release.
1539 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1540 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1541 use expasy mirrors or EBI dbfetch cgi-script.
1543 o A moderate number of documentation improvements were made as
1544 well to provide a better code synopsis in each module.
1547 0.7 Large number of changes, including refactoring of the
1548 Object system, new parsers, new functionality and
1549 all round better system. Highlights are:
1552 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1553 Bio::Root::IO for I/O and file/handle capabilities.
1555 o Imported BPlite modules from Ian Korf for BLAST
1556 parsing. This is considered the supported BLAST parser;
1557 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1559 o Improved Sequence Feature model. Added complete location
1560 modelling (with fuzzy and compound locations). See
1561 Bio::LocationI and the modules under Bio/Location. Added
1562 support in Genbank/EMBL format parsing to completely parse
1563 feature tables for complex locations.
1565 o Moved special support for databanks etc to specialized modules under
1566 Bio/Seq/. One of these supports very large sequences through
1567 a temporary file as a backend.
1569 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1570 CDS retrieval and exon shuffling.
1572 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1574 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1575 DB/GDB (the latter has platform-specific limitations).
1577 o New analysis parser framework for HT sequence annotation (see
1578 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1580 o New Alignment IO framework
1582 o New Index modules (Swissprot)
1584 o New modules for running Blast within perl
1585 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1586 Multiple Sequence Alignment tools ClustalW and TCoffee
1587 (Bio::Tools::Run::Alignment).
1589 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1590 documentation across the package.
1592 o Much improved cross platform support. Many known incompatibilities
1593 have been fixed; however, NT and Mac do not work across the entire
1594 setup (see PLATFORMS).
1596 o Many bug fixes, code restructuring, etc. Overall stability and
1597 maintainability benefit a lot.
1599 o A total of 957 automatic tests
1604 There are very few functionality changes but a large
1605 number of software improvements/bug fixes across the package.
1607 o The EMBL/GenBank parsing are improved.
1609 o The Swissprot reading is improved. Swissprot writing
1610 is disabled as it doesn't work at all. This needs to
1611 wait for 0.7 release
1613 o BLAST reports with no hits are correctly parsed.
1615 o Several other bugs of the BLAST parser (regular expressions, ...)
1618 o Old syntax calls have been replaced with more modern syntax
1620 o Modules that did not work at all, in particular the Sim4
1621 set have been removed
1623 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1624 have improved compliance with interface specs and documentation
1626 o Mailing list documentation updated throughout the distribution
1628 o Most minor bug fixes have happened.
1630 o The scripts in /examples now work and have the modern syntax
1631 rather than the deprecated syntax
1634 0.6.1 Sun April 2 2000
1636 o Sequences can have Sequence Features attached to them
1637 - The sequence features can be read from or written to
1638 EMBL and GenBank style flat files
1640 o Objects for Annotation, including References (but not
1641 full medline abstracts), Database links and Comments are
1644 o A Species object to represent nodes on a taxonomy tree
1647 o The ability to parse HMMER and Sim4 output has been added
1649 o The Blast parsing has been improved, with better PSI-BLAST
1650 support and better overall behaviour.
1652 o Flat file indexed databases provide both random access
1653 and sequential access to their component sequences.
1655 o A CodonTable object has been written with all known
1656 CodonTables accessible.
1658 o A number of new lightweight analysis tools have been
1659 added, such as molecular weight determination.
1661 The 0.6 release also has improved software engineering
1663 o The sequence objects have been rewritten, providing more
1664 maintainable and easier to implement objects. These
1665 objects are backwardly compatible with the 0.05.1 objects
1667 o Many objects are defined in terms of interfaces and then
1668 a Perl implementation has been provided. The interfaces
1669 are found in the 'I' files (module names ending in 'I').
1671 This means that it is possible to wrap C/CORBA/SQL access
1672 as true "bioperl" objects, compatible with the rest of
1675 o The SeqIO system has been overhauled to provide better
1676 processing and perl-like automatic interpretation of <>
1679 o Many more tests have been added (a total of 172 automatic
1680 tests are now run before release).
1684 0.05.1 Tue Jun 29 05:30:44 1999
1685 - Central distribution now requires Perl 5.004. This was
1686 done to get around 5.003-based problems in Bio/Index/*
1688 - Various bug fixes in the Bio::Tools::Blast modules
1689 including better exception handling and PSI-Blast
1690 support. See Bio/Tools/Blast/CHANGES for more.
1691 - Fixed the Parse mechanism in Seq.pm to use readseq.
1692 Follow the instructions in README for how to install
1693 it (basically, you have to edit Parse.pm).
1694 - Improved documentation of Seq.pm, indicating where
1695 objects are returned and where strings are returned.
1696 - Fixed uninitialized warnings in Bio::Root::Object.pm
1697 and Bio::Tools::SeqPattern.pm.
1698 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1700 0.05 Sun Apr 25 01:14:11 1999
1701 - Bio::Tools::Blast modules have less memory problems
1702 and faster parsing. Webblast uses LWP and supports
1703 more functionality. See Bio/Tools/Blast/CHANGES for more.
1704 - The Bio::SeqIO system has been started, moving the
1705 sequence reformatting code out of the sequence object
1706 - The Bio::Index:: system has been started, providing
1707 generic index capabilities and specifically works for
1708 Fasta formatted databases and EMBL .dat formatted
1710 - The Bio::DB:: system started, providing access to
1711 databases, both via flat file + index (see above) and
1713 - The scripts/ directory, where industrial strength scripts
1714 are put has been started.
1715 - Many changes - a better distribution all round.
1717 0.04.4 Wed Feb 17 02:20:13 1999
1718 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1719 (see Bio::Tools::Blast::CHANGES).
1720 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1721 - Beefed up the t/Fasta.t test script.
1722 - Small fix in Bio::Seq::type() (now always returns a string).
1723 - Changed Bio::Root::Utilities::get_newline_char() to
1724 get_newline() since it could return more than one char.
1725 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1726 - Changed default timeout to 20 seconds (was 3).
1727 - Moved lengthy modification notes to the bottom of some files.
1728 - Fixed SimpleAlign write_fasta bug.
1729 - Beefed up SimpleAlign.t test
1731 0.04.3 Thu Feb 4 07:48:53 1999
1732 - Bio::Root::Object.pm and Global.pm now detect when
1733 script is run as a CGI and suppress output that is only
1734 appropriate when running interactively.
1735 - Bio::Root::Err::_set_context() adds name of script ($0).
1736 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1737 regarding the use of the static objects via the qw(:obj) tag.
1738 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1739 CORE::reverse, avoiding Perl warnings.
1740 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1741 example scripts (see Bio::Tools::Blast::CHANGES).
1742 - examples/seq/seqtools.pl no longer always warns about using
1743 -prot or -nucl command-line arguments; only when using the
1745 - Methods added to Bio::Root::Utilities: create_filehandle(),
1746 get_newline_char(), and taste_file() to generalize filehandle
1747 creation and autodetect newline characters in files/streams
1748 (see bug report #19).
1749 - Bio::Root::IOManager::read() now handles timeouts and uses
1750 Utilities::create_filehandle().
1751 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1752 of hardwiring in "\n".
1753 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1755 0.04.2 Wed Dec 30 02:27:36 1998
1756 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1757 (see Bio::Tools::Blast::CHANGES).
1758 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1759 to CORE::reverse (prevents ambiguous warnings with 5.005).
1760 - Appending '.tmp.bioperl' to temporary files created by
1761 Bio::Root::Utilities::compress() or uncompress() to
1762 make it easy to identify & cleanup these files as needed.
1763 - Developers: Created CVS branch release-0-04-bug from
1764 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1765 be sure to cvs checkout this branch into a clean area.
1767 0.04.1 Wed Dec 16 05:39:15 1998
1768 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1769 (see Bio::Tools::Blast::CHANGES).
1770 - Compile/SW/Makefile.PL now removes *.o and *.a files
1773 0.04 Tue Dec 8 07:49:19 1998
1774 - Lots of new modules added including:
1775 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1776 and Bio/Compile directory containing XS-linked C code for
1777 creating Smith-Waterman sequence alignments from within Perl.
1778 * Steve Chervitz's Blast distribution has been incorporated.
1779 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1780 - Bio/examples directory for demo scripts for all included modules.
1781 - Bio/t directory containing test suit for all included modules.
1782 - For changes specific to the Blast-related modules prior to
1783 incorporation in this central distribution, see the CHANGES
1784 file in the Bio/Tools/Blast directory.
1786 0.01 Tue Sep 8 14:23:22 1998
1787 - original version from central CVS tree; created by h2xs 1.18