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://redmine.open-bio.org/projects/bioperl
17 CPAN releases are branched from 'master'.
18 ---------------------------------------------------------
24 * Bio::Search::HSP::GenericHSP
25 - Bug #3370, added a "posterior_string" method to retrieve the
26 posterior probability lines (PP) from HMMER3 reports [fjossandon]
27 - Added a "consensus_string" method to retrieve the consensus
28 structure lines (CS|RF) from HMMER2 and HMMER3 reports when available [fjossandon]
29 * Bio::SearchIO::hmmer2
30 - The number of identical and conserved residues are now calculated
31 directly from the homology line [fjossandon]
32 - Now the Query Length and Hit Length are reported when the alignment
33 runs until the end of the sequence/model ('.]' or '[]') [fjossandon]
34 - Implemented the capture of the consensus structure lines [fjossandon]
35 * Bio::SearchIO::hmmer3
36 - The number of identical and conserved residues are now calculated
37 directly from the homology line [fjossandon]
38 - Now the Hit Length is reported when the alignment runs until the end
39 of the sequence/model ('.]' or '[]') [fjossandon]
40 - Implemented the capture of the consensus structure lines [fjossandon]
41 - Implemented the capture of the posterior probability lines [fjossandon]
42 - Completed the development of NHMMER parsing, including alignments [fjossandon]
43 * Bio::SearchIO::SearchResultEventBuilder & Bio::SearchIO::IteratedSearchResultEventBuilder
44 - Feature #2615, moved "_init_parse_params", "max_significance, "signif",
45 "min_score", "min_bits, and "hit_filter" methods from
46 'IteratedSearchResultEventBuilder' to parent 'SearchResultEventBuilder'.
47 This means that the Bio::SearchIO->new() parameters '-signif', '-score',
48 '-bits' and '-hit_filter' will now work with other Bio::SearchIO formats
49 besides Blast, instead of being ignored. Added tests for all moved methods
50 using HMMER outputs and run the full test suite and everything pass [fjossandon]
54 * GenericHSP: Added '.' to gap symbols in "_pre_gaps" (except for ERPIN),
55 since it is now used by HMMER3 format in alignments [fjossandon]
56 * GenericHit: Changed "frac_aligned_query" and "frac_aligned_hit"
57 to return undef if the query/hit length is unknown (like in some
58 HMMER outputs), to avoid division by 0 crashes. Also "query_length"
59 now is set to 0 if its undefined, to be consistent with hit "length" [fjossandon]
60 * HMMER: fixed many bugs in the parsing of Hmmer2 and Hmmer3 outputs,
61 added support to multi-query reports, reduced code redundancy,
62 and eliminated the automatic removal of hits below "inclusion threshold" [fjossandon]
63 * [3369] - Fixed reported bugs in parse from HMMSEARCH3 reports [fjossandon]
64 * [3446] - Fixed wrong marker position in Bio::Map::Physical [fjossandon]
65 * [3455] - Fixed wrong print of DBLink in Genbank file [bosborne]
66 * Fixed some Bio::Root::Utilities subroutines [fjossandon]
67 * Double-quotes on paths are needed in some places [fjossandon]
68 * [3453] - Allow multiple homologies and products in Entrezgene [fjossandon]
69 * Use "NUL" instead of"/dev/null" when running in Windows [fjossandon]
70 * Updated all files from Bio-Root, Bio-Coordinate and Bio-SearchIO-blastxml
71 with the latest changes made in their own repositories [fjossandon]
72 * General synching of files with the master branch [fjossandon]
73 * Fixed tests failing in Windows because of using Linux commands [fjossandon]
74 * Closed many open filehandles that prevented temporary files deletion [fjossandon]
75 * Fixed broken MeSH parser [fjossandon]
79 * Major Windows support updates! [fjossandon]
80 * MAKER update to allow for stricter standard codon table [cjfields]
81 * Better support for circular sequences [fjossandon]
82 * Fixes for some complex location types [fjossandon]
83 * Address CONTIG bug in GenBank format, bug #3448 [cjfields]
84 * Fix bug #2978 related to BLAST report type [fjossandon]
85 * Deobfuscator fixes [DaveMessina]
89 * Address CPAN test failures [cjfields]
90 * Add BIOPROJECT support for Genbank files [hyphaltip]
91 * Better regex support for HMMER3 output [bosborne]
95 * Minor update to address CPAN test failures
99 * Remove Bio::Biblio and related files [carandraug]
100 - this cause version clashes with an independently-released
101 version of Bio::Biblio
107 * Hash randomization fixes for perl 5.18.x
108 - Note: at least one module (Bio::Map::Physical) still has a failing test;
109 this is documented in bug #3446 and has been TODO'd; we will be pulling
110 Bio::Map and similar modules out of core into separate distributions in the
111 1.7.x release series [cjfields]
115 * Bio::Seq::SimulatedRead
116 - New module to represent reads taken from other sequences [fangly]
118 - Support of Clone::Fast as a faster cloning alternative [fangly]
120 - Moved the format() and variant() methods from Bio::*IO modules to
121 Bio::Root::IO [fangly]
122 - Can now use format() to get the type of IO format in use [fangly]
124 - New regexp() method to create regular expressions from IUPAC sequences
126 * Bio::SeqFeature::Primer and Bio::Seq::PrimedSeq:
127 - Code refresh [fangly]
129 - Added support for the Greengenes and Silva taxonomies [fangly]
130 * Bio::Tree::TreeFunctionsI
131 - get_lineage_string() represents a lineage as a string [fangly]
132 - add_trait() returns instead of reporting an error when the column
133 number is exceeded in add_trait() [fangly]
134 - Option to support tree leaves without trait [fangly]
135 - Allow ID of 0 in trait files [fangly]
136 * Bio::DB::Taxonomy::list
137 - Misc optimizations [fangly]
138 - Option -names of get_taxon() to help with ambiguous taxa [fangly]
139 * Bio::DB::Taxonomy::*
140 - get_num_taxa() returns the number of taxa in the database [fangly]
141 * Bio::DB::Fasta and Bio::DB::Qual
142 - support indexing an arbitrary list of files [fangly]
143 - user can supply an arbitrary index file name [fangly]
144 - new option to remove index file at the end [fangly]
146 - now handles IUPAC degenerate residues [fangly]
147 * Bio::PrimarySeq and Bio::PrimarySeqI
148 - speed improvements for large sequences [Ben Woodcroft, fangly]
150 - tightened and optimized quality string validation [fangly]
152 - new method and option 'block', to create FASTA output with space
153 intervaled blocks (similar to genbank or EMBL) has been implemented.
154 - package variables $WIDTH and $DEFAULT_SEQ_ID_TYPE have been removed
155 in favour of the methods 'width' and 'preferred_id_type` respectively.
157 - moved from bioperl-live into the separate distribution Bio-FeatureIO
158 * Bio::SeqFeature::Annotated
159 - moved from bioperl-live into the separate distribution Bio-FeatureIO
160 * Bio::Cluster::SequenceFamily
161 - improved performance when using get_members with overlapping multiple
163 * Bio::SearchIO::hmmer3
164 - now supports nhmmer [bosborne]
168 * [3302] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse
169 multi-query hmmer output [Francisco J. Ossandon, Paul Cantalupo]
170 * [3421] Fixes bug in Bio::SearchIO::hmmer2.pm to correctly parse an HSP
171 with a line full of dashes [Francisco J. Ossandon, Paul Cantalupo]
172 * [3298] Fix bug in Bio::SearchIO::blast.pm where algorithm version
173 information was lost in a multi-result blast file [Paul Cantalupo]
174 * [3343] Fix bug in Bio::SearchIO::blasttable.pm to correctly calculate
175 total gaps [Paul Cantalupo]
176 * [3375] Fix DBLINK parsing bug in Bio::SeqIO::genbank.pm [Paul Cantalupo]
177 * [3376] Fix bug in Bio::SearchIO::hmmer2.pm to correctly handle case
178 when end of domain indicator is split across lines [Paul Cantalupo]
179 * [3240] Bio::AlignIO::stockholm now parses simple sequences [Bernd Web,
181 * [3237] Bio::DB::Fasta now allows blank lines between sequences, catches
182 instances where blank lines are within sequences [cjfields]
183 * Bio::DB::Fasta reports correct alphabet for files with multiple sequence
185 * Bio::DB::Fasta rev-comps sequences other than DNA properly [fangly]
186 * [3238] Fixes for Bio::DB::SeqFeature::Store::DBI::Pg [Thomas Burkhard,
188 * Various fixes for Stockholm file indexing and processing [bosborne]
189 * Fix edge case in FASTQ parsing where sequence of length 1 and qual of 0
190 breaks parsing [cjfields]
191 * Fix case where Bio::Seq::Meta* objects with no meta information could not
192 be reverse-complemented [fangly]
193 * Fix bug for fields without aliases in Bio::DB::Query::HIVQuery [fangly]
194 * Fix Bio::PopGen::IO::phase: sort values lexically instead of numerically
195 when unsure that values will be numerical [fangly]
196 * Fix undef warnings in Bio::SeqIO::embl [fangly]
197 * Fix undef warnings in Bio::DB::Fasta and Bio::DB::Qual [fangly]
198 * Fix Bio::Tools::IUPAC should accept any sequence object [fangly]
199 * Fix for 'Inappropriate ioctl' in Bio::DB::Store::berkeleydb3 [Olivier
201 * Bio::SeqFeature::Generic SeqfeatureI compliance: methods primary_tag,
202 source_tag and display_name must return a string, not undef [fangly]
203 * Bio::SimpleAlign and Bio::Seq compliance with Bio::FeatureHolderI
204 add_SeqFeature takes a single argument [fangly]
205 * Use cross-platform filenames and temporary directory in
206 Bio::DB::Taxonomy::flatfile [fangly]
207 * Fix bug in Bio::DB::Taxonomy::list where taxa with no ancestors were not
208 properly identified as existing taxa in the database [fangly]
209 * Fix issue where a Bio::DB::Taxonomy::list object could not be created
210 without also passing a lineage to store [fangly]
211 * Prevent passing a directory to the gi2taxid option (-g) of
212 bp_classify_hits_kingdom.pl and remove an 'earlier declaration' warning
214 * Fixed bp_genbank2gff3.pl crash when missing source feature date [fangly]
215 * Bio::PrimarySeq constructor -direct works for -seq or -ref_to_seq [fangly]
216 * Bio::Cluster::SequenceFamily - checks if the sequence has a Bio::Species
217 object before trying to access, and no longer returns repeated sequences.
224 * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
225 modules using Ace will also be deprecated [lds, cjfields]
226 * Minor bug fix release
227 * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
228 * Address Build.PL issues when DBI is not present [hartzell]
229 * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
230 * Remove deprecated code for perl 5.14.0 compat [cjfields]
231 * Due to schema changes and lack of support for older versions, support
232 for NeXML 0.9 is only (very) partially implemented.
233 See: https://redmine.open-bio.org/issues/3207
237 * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
238 docs [genehack, cjfields]
239 * $VERSION for CPAN/cpanm-based installs was broken; force setting of
240 module version from dist_version (probably not the best way to do this,
241 but it seems to work) [rbuels, cjfields]
244 1.6.900 April 14, 201
248 * This will probably be the last release to add significant features to
249 core modules; subsequent releases will be for bug fixes alone.
250 We are planning on a restructuring of core for summer 2011, potentially
251 as part of the Google Summer of Code. This may become BioPerl 2.0.
252 * Version bump represents 'just prior to v 1.7'. We may have point
253 releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
254 This code essentially is what is on the github master branch.
258 * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
260 - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
261 - removal of Scalar::Util::weaken code, which was causing odd headaches
262 with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
263 * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
265 * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
268 - bug 2515 - new contribution [Ryan Golhar, jhannah]
270 - support for reading Maq, Sam and Bowtie files [maj]
271 - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
272 - bug 2483: support for writing ACE files [Joshua Udall, fangly]
273 - bug 2599: support DBLINK annotation in GenBank files [cjfields]
274 - bug 2726: reading/writing granularity: whole scaffold or one contig
275 at a time [Joshua Udall, fangly]
277 - Added parsing of xrefs to OBO files, which are stored as secondary
278 dbxrefs of the cvterm [Naama Menda]
279 - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
280 * PAML code updated to work with PAML 4.4d [DaveMessina]
284 * [3198] - sort tabular BLAST hits by score [DaveMessina]
285 * [3196] - fix invalid metadata produced by latest Module::Build [cjfields]
286 * [3190] - RemoteBlast GAPCOSTS regex fix [Ali Walsh, cjfields]
287 * [3185] - Bio::Tools::SeqStats->get_mol_wt now gives correct MW
289 * [3178] - fix tr/// issue in Bio::Range [Andrew Conley, cjfields]
290 * [3172] - Bio::DB::Fasta - catch possibly bad FASTA files [cjfields]
291 * [3164] - TreeFunctionsI syntax bug [gjuggler]
292 * [3163] - AssemblyIO speedup [fangly]
293 * [3160] - Bio::SearchIO::Writer::TextResultWriter output [Paul Cantalupo,
295 * [3159] - add SwissPfam support to bp_index.PLS [hyphaltip]
296 * [3158] - fix EMBL file mis-parsing [cjfields]
297 * [3157] - Bio::Restriction::Analysis 'sizes' method fixed [Marc Perry,
299 * [3153] - fix SeqIO::swiss TagTree issues [Charles Tilford, cjfields]
300 * [3148] - URL change for UniProt [cjfields]
301 * [3145] - AXT off-by-1 error [Aaron Goodman, cjfields]
302 * [3136] - HMMer3 parser fixes [kblin]
303 * [3126] - catch description [Toshihiko Akiba]
304 * [3122] - Catch instances where non-seekable filehandles were being
305 seek'd w/o checking for status [Stefan Kirov, Roy Chaudhuri]
306 * [3121] - Bio::OntologyIO cannot parse the full InterPro XML file
307 [dukeleto, rbuels, cjfields]
308 * [3120] - bp_seqfeature_gff3.pl round-trip fixes [genehack, David Breimann,
310 * [3116,3117] - perl 5.12.x warnings fixed [cjfields, Charles Tilford]
311 * [3110] - Better 'namespace' support for bp_seqfeature_load.PLS [dbolser,
313 * [3107] - BLAST alignment column_from_residue_number() [cjfields]
314 * [3104] - Bio::Species single node hierarchies [Charles Tilford, cjfields]
315 * [3092, 3090] - parsing of BLAST HSP stats [Razi Khaja, cjfields]
316 * [3089] - HSPTableWriter missing methods [Robson de Souza, cjfields]
317 * [3086] - EMBL misparsing long tags [kblin, cjfields]
318 * [3085] - CommandExts and array of files [maj, hyphaltip]
319 * [3077] - Bio::SimpleAlign slice() now correctly computes seq coordinates
320 for alignment slices [Ha X. Dang, cjfields]
321 * [3076] - XMFA alignment strand wrong [Ha X., cjfields]
322 * [3073] - fix parsing of GenBank files from RDP [cjfields]
323 * [3068] - FASTQ parse failure with trailing 0 [cjfields]
324 * [3064] - All-gap midline BLAST report issues [cjfields]
325 * [3063] - BLASt report RID [Razi Khaja, cjfields]
326 * [3058] - SearchIO::fasta parsing [DaveMessina, cjfields]
327 * [3053] - LOCUS line formatting [M. Wayne, cjfields]
328 * [3039] - correct Newick output root node branch length [gjuggler,
330 * [3038] - SELEX alignment error [Bernd, cjfields]
331 * [3033] - PrimarySeq ID setting [Bernd, maj]
332 * [3032] - Fgenesh errors [Wes Barris, hyphaltip]
333 * [3034] - AlignIO::clustal output [Bernd, DaveMessina]
334 * [3031] - Parse algorithm ref for BLAST [Razi Khaja, cjfields]
335 * [3028] - Bio::TreeIO::nexus and FigTree compat [Kevin Balbi, cjfields]
336 * [3025] - Bio::SeqIO::embl infinite loop [Adam Sjøgren, cjfields]
337 * [3040, 3023, 2974, 2921, 2753, 2636, 2482] - PAML parser fixed, works with
338 PAML 4.4d [DaveMessina]
339 * [3015, 3022] - Bio::Restriction withrefm regexp [Emmanuel Quevillon,
341 * [3020] - GFF3Loader alias attribute [Nathan Weeks, cjfields]
342 * [3018, 3019, 3021] - gmap_f9 parsing [Kiran Mukhyala, cjfields]
343 * [3017] - using threads with Bio::DB::GenBank [cjfields]
344 * [3012] - Bio::Root::HTTPget fixes [maj, cjfields]
345 * [3011] - namespace support for SF::Store::DBI::Pg [Adam Witney, cjfields]
346 * [3002] - Bio::DB::EUtilities NCBI policy updates [cjfields]
347 * [3001] - seq identifier '0' dropped with FASTA [Michael Kuhn, maj]
348 * [2984] - let LocatableSeq decide on length of phylip aln [Adam Witney,
350 * [2983] - fix score/percent ID mixup [Alexie Papanicolaou]
351 * [2977] - TreeIO issues [DaveMessina]
352 * [2959] - Bio::SeqUtils->revcom_with_features [Roy Chaudhuri, maj]
353 * [2944] - Bio::Tools::GFF score [cjfields]
354 * [2942] - correct MapTiling output [maj]
355 * [2939] - PDB residue insertion codes [John May, maj]
356 * [2930] - PrimarySeqI term symbol [Adam Sjøgren, maj]
357 * [2928] - GuessSeqFormat raw [maj]
358 * [2926] - Bio:Tools::TandemRepeatsFinder seq_id [takadonet, cjfields]
359 * [2922] - open() directive issue [cjfields]
360 * [2915] - GenBank parser infinite loop [Francisco Ossandon, cjfields]
361 * [2901] - DNAStatistics div by zero error [Janet Young, cjfields]
362 * [2899] - SeqFeature::Store host issues [lstein, dbolser]
363 * [2897] - Add a "mask_below_threshold" method to Seq::Quality [dbolser,
365 * [2881] - .scf files don't' roundtrip [Adam Sjøgren, cjfields]
366 * [2876] - CDD search with RemoteBlast [Malcolm Cook]
367 * [2863] - Root::IO::_initialize_io causes crash [rbuels, maj, DaveMessina]
368 * [2845] - Bio::Seq::Quality gives seq with no ID [Tristan Lefebure, cjfields]
369 * [2843] - FeatureIO BED to GFF fails w/ no phase [cassjm cjfields]
370 * [2773] - Bio::Tree::Node premature GC [Morgan Price, cjfields]
371 * [2764] - add ID Tracker helper for SwissProt [heikki, cjfields]
372 * [2758] - Bio::AssemblyIO ace problems [fangly]
373 * [2744] - Bio::LocatableSeq::end [Bernd, cjfields]
374 * [2726] - ace file IO [Josh, fangly]
375 * [2700] - Refactor Build.PL [cjfields]
376 * [2673] - addition of simple Root-based clone() method [cjfields]
377 * [2648] - Bio::Assembly::Scaffold->get_all_seq_ids [dbolser, fangly]
378 * [2599] - support for DBLINK annotation in GenBank files [cjfields]
379 * [2594] - Bio::Species memory leak [cjfields]
380 * [2515] - GenBank XML parser [jhannah]
381 * [2499] - Method "pi" in package Bio::PopGen::Statistics [hyphaltip]
382 * [2483] - Bio::Assembly::IO::ace write_assembly implemented [fangly]
383 * [2350] - ID consistency btwn Bio::SeqI, Bio::Align::AlignI [fangly,
385 * [1572] - no docs Bio::Location::Simple/Atomic::trunc [hyphaltip]
389 * Bio::Expression modules - these were originally designed to go with the
390 bioperl-microarray suite of tools, however they have never been completed
391 and so have been removed from the distribution. The original code has
392 been moved into the inactive bioperl-microarray suite. [cjfields]
396 * Repository moved from Subversion (SVN) to
397 http://github.com/bioperl/bioperl-live [cjfields]
398 * Bug database has moved to Redmine (https://redmine.open-bio.org)
399 * Bio::Micrarray - the tools developed for ReSeq chip analysis by Marian
400 Thieme have been moved to their own distribution (Bio-Microarray).
403 1.6.1 Sept. 29, 2009 (point release)
404 * No change from last alpha except VERSION and doc updates [cjfields]
406 1.6.0_6 Sept. 27, 2009 (sixth 1.6.1 alpha)
407 * Fix for silent OBDA bug related to FASTA validation [cjfields]
409 1.6.0_5 Sept. 27, 2009 (fifth 1.6.1 alpha)
410 * Possible fix for RT 49950 (Strawberry Perl installation) [cjfields]
411 * [RT 50048] - removed redundant VERSION, which was borking CPANPLUS
413 * BioPerl.pod -> BioPerl.pm (Perl Best Practices) [cjfields]
415 1.6.0_4 Sept. 25, 2009 (fourth 1.6.1 alpha)
416 * WinXP test fixes [cjfields, maj]
417 * BioPerl.pod added for descriptive information, fixes CPAN indexing
419 * Minor doc fixes [cjfields]
421 1.6.0_3 Sept. 22, 2009 (third 1.6.1 alpha)
422 * Fix tests failing due to merging issues [cjfields]
423 * More documentation updates for POD parsing [cjfields]
425 1.6.0_2 Sept. 22, 2009 (second 1.6.1 alpha)
427 - fix YAML meta data generation [cjfields]
429 1.6.0_1 Sept. 15, 2009 (first 1.6.1 alpha)
430 * Bio::Align::DNAStatistics
431 - fix divide by zero problem [jason]
433 - bug 2813 - fix faulty logic to detect end-of-stream [cjfields]
434 * Bio::AlignIO::stockholm
435 - bug 2796 - fix faulty logic to detect end-of-stream [cjfields]
436 * Bio::Assembly::Tools::ContigSpectrum
437 - function to score contig spectrum [fangly]
438 * Bio::DB::EUtilities
439 - small updates [cjfields]
441 - berkeleydb database now autoindexes wig files and locks correctly
444 - various small updates for stability; tracking changes to LANL
445 database interface [maj]
446 * Bio::DB::SeqFeature (lots of updates and changes)
447 - add Pg, SQLite, and faster BerkeleyDB implementations [lstein, scain]
448 - bug 2835 - patch [Dan Bolser]
449 - bug RT 44535 - patch FeatureFileLoader [Cathy Gresham]
451 - bug 2764 - idtracker() method [cjfields, courtesy Neil Saunders]
452 * Bio::Factory::FTLocationFactory
453 - mailing list bug fix [cjfields]
455 - performance work on column_from_residue_number [hartzell]
456 * Bio::Matrix::IO::phylip
457 - bug 2800 - patch to fix phylip parsing [Wei Zou]
459 - Google Summer of Code project from Chase Miller - parsers for Nexml
460 file format [maj, chmille4]
462 - Make Individual, Population, Marker objects AnnotatableI [maj]
463 - simplify LD code [jason]
465 - deal with empty intersection [jason]
467 - significant overhaul of Bio::Restriction system: complete support for
468 external and non-palindromic cutters. [maj]
470 - CPANPLUS support, no automatic installation [sendu]
472 - allow IO::String (regression fix) [cjfields]
473 - catch unintentional undef values [cjfields]
474 - throw if non-fh is passed to -fh [maj]
475 * Bio::Root::Root/RootI
476 - small debugging and core fixes [cjfields]
478 - bug RT 48813 - fix for Strawberry Perl bug [kmx]
479 * Bio::Root::Utilities
480 - bug 2737 - better warnings [cjfields]
482 - tiling completely refactored, HOWTO added [maj]
483 NOTE : Bio::Search::Hit::* classes do not use this code directly; we
484 will deprecate usage of the older tiling code in the next BioPerl
486 - small fixes [cjfields]
488 - Infernal 1.0 output now parsed [cjfields]
489 - new parser for gmap -f9 output [hartzell]
490 - bug 2852 - fix infinite loop in some output [cjfields]
491 - blastxml output now passes all TODO tests [cjfields]
492 - bug 2346, 2850 - psl and exonerate parsing fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
493 - RT 44782 - GbrowseGFF writer now catches evalues [Allen Day]
494 - bug 2575 - add two columns of additional output to HSPTableWriter [cjfields]
495 * Bio::Seq::LargePrimarySeq
496 - delete tempdirs [cjfields]
497 - bug fixes [rbuels, jhannah, bvecchi, YAPC hackathon]
499 - extract regions based on quality threshold value [Dan Bolser, heikki]
500 - bug 2847 - resolve threshold issue (rbuels, jhannah, bvecchi)
501 * Bio::SeqFeature::Lite
502 - various Bio::DB::SeqFeature-related fixes [lstein]
503 * Bio::SeqFeature::Tools::TypeMapper
504 - additional terms for GenBank to SO map [scain]
505 * Bio::SeqIO::chadoxml
506 - bug 2785 - patch to get this working for bp_seqconvert [cjfields]
508 - support for CDS records [dave_messina, Sylvia]
510 - complete refactoring to handle all FASTQ variants, perform validation,
511 write output. API now conforms with other Bio* parsers and the rest of
512 Bio::SeqIO (e.g. write_seq() creates fastq output, not fasta output).
514 * Bio::SeqIO::genbank
515 - bug 2784 - fix DBSOURCE issue [Phillip Garland]
516 - bug RT 44536 - support for UniProt/UniProtKB tests [cjfields]
517 * Bio::SeqIO::largefasta
518 - parser returns a Bio::Seq::LargePrimarySeq [jhannah]
520 - add option for 'single' and 'multiple'
522 - bug 2881 - fix scf round-tripping [Adam Søgren]
524 - bug 2766, 2810 - copy over tags from features, doc fixes [David
527 - bug 2793 - patch for add_seq index issue [jhannah, maj]
528 - bug 2801 - throw if args are required [cjfields]
529 - bug 2805 - uniq_seq returns SimpleAlign and hash ref of sequence types
530 [Tristan Lefebure, maj]
531 - bug fixes from YAPC hackathon [rbuels, jhannah, bvecchi]
532 - fix POD and add get_SeqFeatures filter [maj]
533 * Bio::Tools::dpAlign
534 - add support for LocatableSeq [ymc]
535 - to be moved to a separate distribution [cjfields, rbuels]
536 * Bio::Tools::EUtilities
537 - fix for two bugs from mail list [Adam Whitney, cjfields]
538 - add generic ItemContainerI interface for containing same methods
541 - fix up code, add more warnings [cjfields]
542 - to be moved to a separate distribution [cjfields, rbuels]
543 * Bio::Tools::Primer3
544 - bug 2862 - fenceposting issue fixed [maj]
545 * Bio::Tools::Run::RemoteBlast
546 - tests for remote RPS-BLAST [mcook]
547 * Bio::Tools::SeqPattern
548 - bug 2844 - backtranslate method [rbuels, jhannah, bvecchi]
549 * Bio::Tools::tRNAscanSE
550 - use 'gene' and 'exon' for proper SO, ensure ID is unique [jason]
552 - bug 2456 - fix reroot_tree(), added create_node_on_branch() [maj]
553 * Bio::Tree::Statistics
554 - several methods for calculating Fitch-based score, internal trait
555 values, statratio(), sum of leaf distances [heikki]
557 - bug 2869 - add docs indicating edge case where nodes can be
558 prematurely garbage-collected [cjfields]
559 - add as_text() function to create Tree as a string in specified format
561 * Bio::Tree::TreeFunctionsI
562 - bug 2877 - fix bug where bootstrap assigned to the wrong node [Tristan
564 * Bio::TreeIO::newick
565 - fix small semicolon issue [cjfields]
567 - update to bp_seqfeature_load for SQLite [lstein]
568 - hivq.pl - commmand-line interface to Bio::DB::HIV [maj]
569 - fastam9_to_table - fix for MPI output [jason]
570 - gccalc - total stats [jason]
572 - POD cleanup re: FEEDBACK section [maj, cjfields]
573 - cleanup or fix dead links [cjfields]
574 - Use of no_* methods (indicating 'number of something') is deprecated
575 in favor of num_* [cjfields]
576 - lots of new tests for the above bugs and refactors [everyone!]
577 - new template for Komodo text editor [cjfields]
580 * Feature/Annotation rollback
581 - Problematic changes introduced prior to the 1.5 release have been
582 rolled back. These changes led to subtle bugs involving operator
583 overloading and interface methods.
584 - Behavior is very similar to that for BioPerl 1.4, with tag values
585 being stored generically as simple scalars. Results in a modest
588 - Split into a separate distribution on CPAN, primarily so development
589 isn't reliant on a complete BioPerl release.
590 - Bio::Graphics::Pictogram has been renamed to Bio::Draw::Pictogram but
591 is only available via Subversion (via bioperl-live main trunk)
593 - Common test bed for all BioPerl modules
595 - Common Module::Build-based subclass for all BioPerl modules
596 * Bio::DB::EUtilities
597 - Complete refactoring to split up parsing (Bio::Tools::EUtilities),
598 parameter handling (Bio::Tools::EUtilities::EUtilParameters),
599 and user agent request posting and retrieval
600 * Test implementation and reorganization
601 - Tests have been reorganized into groups based on classes or use
603 - Automated test coverage is now online:
604 http://www.bioperl.org/wiki/Test_Coverage
605 - After this release, untested modules will be moved into a
606 separate developer distribution until tests can be derived.
607 Also, new modules to be added are expected to have a test suite
608 and adequate test coverage.
610 1.5.2 Developer release
612 Full details of changes since 1.5.1 are available online at:
613 http://www.bioperl.org/wiki/Change_log
614 The following represents a brief overview of the most important changes.
617 - Overhaul. Brand new system fully allows markers to have multiple
618 positions on multiple maps, and to have relative positions. Should be
622 - This module and all the modules in the Taxonomy directory now
623 deprecated in favour of Bio::Taxon and Bio::Tree::Tree
628 * get_Taxonomy_Node() eventually to be deprecated, renamed get_taxon().
630 * New methods ancestor(), each_Descendent() and _handle_internal_id().
632 * Allows for different database modules to create Bio::Taxon objects
633 with the same internal id when the same taxon is requested from each.
636 * get_Children_Taxids() is deprecated, superceded by each_Descendent().
638 * No longer includes the fake root node 'root'; there are multiple roots
639 now (10239, 12884, 12908, 29384 and 131567). Consistent with entrez.pm
642 * get_node() has new option -full
644 * Caches data retrieved from website
647 - Now a Bio::Taxon. Carries out the species name -> specific name munging
648 that Bio::DB::Taxonomy modules and SeqIO modules used to do, for
649 backward compatability in species() method.
651 o Bio::Search and Bio::SearchIO
652 - Overhaul. The existing system has been sped up via some minor changes
653 (mostly gain-of-function to the API). Bio::PullParserI is introduced
654 as a potential eventual replacment for the existing system, though as
655 yet only a Hmmpfam parser exists written using it.
658 1.5.1 Developer release
660 o Major problem with how Annotations were written out with
661 Bio::Seq is fixed by reverting to old behavior for
662 Bio::Annotation objects.
667 * bug #1871; REFLOOP' parsing loop, I changed the pattern to
668 expect at l east 9 spaces at the beginning of a line to
669 indicate line wrapping.
671 * Treat multi-line SOURCE sections correctly, this defect broke
672 both common_name() and classification()
674 * parse swissprot fields in genpept file
676 * parse WGS genbank records
679 * Changed regexp for ID line. The capturing parentheses are
680 the same, the difference is an optional repeated-not-semi-
681 colon expression following the captured \S+. This means the
682 regexp works when the division looks like /PRO;/ or when the
683 division looks like /ANG ;/ - the latter is from EMBL
686 * fix ID line parsing: the molecule string can have spaces in
687 it. Like: "genomic DNA"
689 - swiss.pm: bugs #1727, #1734
692 * Added parser for entrezgene ASN1 (text format) files.
693 Uses Bio::ASN1::EntrezGene as a low level parser (get it from CPAN)
697 - maf.pm coordinate problem fixed
699 o Bio::Taxonomy and Bio::DB::Taxonomy
701 - Parse NCBI XML now so that nearly all the taxonomy up-and-down
702 can be done via Web without downloading all the sequence.
704 o Bio::Tools::Run::RemoteBlast supports more options and complies
705 to changes to the NCBI interface. It is reccomended that you
706 retrieve the data in XML instead of plain-text BLAST report to
707 insure proper parsing and retrieval of all information as NCBI
708 fully expects to change things in the future.
710 o Bio::Tree and Bio::TreeIO
712 - Fixes so that re-rooting a tree works properly
714 - Writing out nhx format from a newick/nexus file will properly output
715 bootstrap information. The use must move the internal node labels over
717 for my $node ( grep { ! $_->is_Leaf } $tree->get_nodes ) {
718 $node->bootstrap($node->id);
721 - Nexus parsing is much more flexible now, does not care about
724 - Cladogram drawing module in Bio::Tree::Draw
726 - Node height and depth now properly calculated
728 - fix tree pruning algorithm so that node with 1 child gets merged
730 o Graphics tweaks. Glyph::xyplot improved. Many other small-medium sized
731 bugs and improvements were added, see Gbrowse mailing list for most of
734 o Bio::DB::GFF partially supports GFF3. See information about
735 gff3_munge flag in scripts/Bio-DB-GFF/bulk_load_gff.pl.
737 o Better location parsing in Bio::Factory::FTLocationFactory -
738 this is part of the engine for parsing EMBL/GenBank feature table
739 locations. Nested join/order-by/complement are allowed now
741 o Bio::PrimarySeqI->translate now takes named parameters
743 o Bio::Tools::Phylo::PAML - parsing RST (ancestral sequence
744 reconstruction) is now supported. Parsing different models and
745 branch specific parametes are now supported.
747 o Bio::Factory::FTLocationFactory - parse hierarchical locations
750 o Bio::Matrix::DistanceMatrix returns arrayrefs instead of arrays
751 for getter/setter functions
755 - blast bug #1739; match scientific notation in score
756 and possible e+ values
758 - blast.pm reads more WU-BLAST parameters and parameters, match
759 a full database pathname,
761 - Handle NCBI WEB and newer BLAST formats specifically
762 (Query|Sbjct:) match in alignment blocks can now be (Query|Sbjct).
764 - psl off-by-one error fixed
766 - exonerate parsing much improved, CIGAR and VULGAR can be parsed
767 and HSPs can be constructed from them.
769 - HSPs query/hit now have a seqdesc field filled out (this was
770 always available via $hit->description and
771 $result->query_description
773 - hmmer.pm can parse -A0 hmmpfam files
775 - Writer::GbrowseGFF more customizeable.
777 o Bio::Tools::Hmmpfam
778 make e-value default score displayed in gff, rather than raw score
779 allow parse of multiple records
782 1.5 Developer release
784 o Bio::Align::DNAStatistics and Bio::Align::ProteinStatistics
785 provide Jukes-Cantor and Kimura pairwise distance methods,
788 o Bio::AlignIO support for "po" format of POA, and "maf";
789 Bio::AlignIO::largemultifasta is a new alternative to
790 Bio::AlignIO::fasta for temporary file-based manipulation of
791 particularly large multiple sequence alignments.
793 o Bio::Assembly::Singlet allows orphan, unassembled sequences to
794 be treated similarly as an assembled contig.
796 o Bio::CodonUsage provides new rare_codon() and probable_codons()
797 methods for identifying particular codons that encode a given
800 o Bio::Coordinate::Utils provides new from_align() method to build
801 a Bio::Coordinate pair directly from a
802 Bio::Align::AlignI-conforming object.
804 o Bio::DB::Biblio::eutils is a class for querying NCBI's Eutils.
805 Send a Pubmed, Pubmed Central, Entrez, or other query to NCBI's
806 web service using standard Pubmed query syntax, and retrieve
809 o Bio::DB::GFF has various sundry bug fixes.
811 o Bio::FeatureIO is a new SeqIO-style subsystem for
812 writing/reading genomic features to/from files. I/O classes
813 exist for BED, GTF (aka GFF v2.5), and GFF v3. Bio::FeatureIO
814 classes only read/write Bio::SeqFeature::Annotated objects.
815 Notably, the GFF v3 class requires features to be typed into the
818 o Bio::Graph namespace contains new modules for manipulation and
819 analysis of protein interaction graphs.
821 o Bio::Graphics has many bug fixes and shiny new glyphs.
823 o Bio::Index::Hmmer and Bio::Index::Qual provide multiple-file
824 indexing for HMMER reports and FASTA qual files, respectively.
826 o Bio::Map::Clone, Bio::Map::Contig, and Bio::Map::FPCMarker are
827 new objects that can be placed within a Bio::Map::MapI-compliant
828 genetic/physical map; Bio::Map::Physical provides a new physical
829 map type; Bio::MapIO::fpc provides finger-printed clone mapping
832 o Bio::Matrix::PSM provide new support for postion-specific
833 (scoring) matrices (e.g. profiles, or "possums").
835 o Bio::Ontology::Ontology and Bio::Ontology::Term objects can now
836 be instantiated without explicitly using Bio::OntologyIO. This
837 is possible through changes to Bio::Ontology::OntologyStore to
838 download ontology files from the web as necessary. Locations of
839 ontology files are hard-coded into
840 Bio::Ontology::DocumentRegistry.
842 o Bio::PopGen includes many new methods and data types for
843 population genetics analyses.
845 o New constructor to Bio::Range, unions(). Given a list of
846 ranges, returns another list of "flattened" ranges --
847 overlapping ranges are merged into a single range with the
848 mininum and maximum coordinates of the entire overlapping group.
850 o Bio::Root::IO now supports -url, in addition to -file and -fh.
851 The new -url argument allows one to specify the network address
852 of a file for input. -url currently only works for GET
853 requests, and thus is read-only.
855 o Bio::SearchIO::hmmer now returns individual Hit objects for each
856 domain alignment (thus containing only one HSP); previously
857 separate alignments would be merged into one hit if the domain
858 involved in the alignments was the same, but this only worked
859 when the repeated domain occured without interruption by any
860 other domain, leading to a confusing mixture of Hit and HSP
863 o Bio::Search::Result::ResultI-compliant report objects now
864 implement the "get_statistics" method to access
865 Bio::Search::StatisticsI objects that encapsulate any
866 statistical parameters associated with the search (e.g. Karlin's
867 lambda for BLAST/FASTA).
869 o Bio::Seq::LargeLocatableSeq combines the functionality already
870 found in Bio::Seq::LargeSeq and Bio::LocatableSeq.
872 o Bio::SeqFeature::Annotated is a replacement for
873 Bio::SeqFeature::Generic. It breaks compliance with the
874 Bio::SeqFeatureI interface because the author was sick of
875 dealing with untyped annotation tags. All
876 Bio::SeqFeature::Annotated annotations are Bio::AnnotationI
877 compliant, and accessible through Bio::Annotation::Collection.
879 o Bio::SeqFeature::Primer implements a Tm() method for primer
880 melting point predictions.
882 o Bio::SeqIO now supports AGAVE, BSML (via SAX), CHAOS-XML,
883 InterProScan-XML, TIGR-XML, and NCBI TinySeq formats.
885 o Bio::Taxonomy::Node now implements the methods necessary for
886 Bio::Species interoperability.
888 o Bio::Tools::CodonTable has new reverse_translate_all() and
889 make_iupac_string() methods.
891 o Bio::Tools::dpAlign now provides sequence profile alignments.
893 o Bio::Tools::GFF now parses GFF version 2.5 (a.k.a. GTF).
895 o Bio::Tools::Fgenesh, Bio::Tools::tRNAscanSE are new report
898 o Bio::Tools::SiRNA includes two new rulesets (Saigo and Tuschl)
899 for designing small inhibitory RNA.
901 o Bio::Tree::DistanceFactory provides NJ and UPGMA tree-building
902 methods based on a distance matrix.
904 o Bio::Tree::Statistics provides an assess_bootstrap() method to
905 calculate bootstrap support values on a guide tree topology,
906 based on provided bootstrap tree topologies.
908 o Bio::TreeIO now supports the Pagel (PAG) tree format.
914 o Improvements to Bio::AlignIO::nexus for parsing TreeBase nexus files
916 o Bio::Graphics will work with gd1 or gd2
919 - hmmer.pm Better hmmpfam parsing, fix bug for small number of alignment outputs
921 - blast.pm Parse multi-line query fields properly
922 - small speed improvements to blasttable.pm and others
924 o Bio::DB::Taxonomy has better support for hierarchy traversal so that
925 Bio::Taxonomy::Node can be as simple as Bio::Species object while still
926 supporting more complex queries
929 1.4. Stable major release
931 Since initial 1.2.0, 3000 separate changes have been made to make this release.
933 o installable scripts
935 o global module version from Bio::Root:Version
938 - major improvements; SVG support
941 - population genetics
942 - support several population genetics types of questions.
943 - Tests for statistical neutrality of mutations
944 (Fu and Li's D/F, Tajima's D) are in Bio::PopGen::Statistics.
945 Tests of population structure (Wright's F-statistic: Fst) is in
946 Bio::PopGen::PopStats. Calculating composite linkage
947 disequilibrium (LD) is available in Bio::PopGen::Statistics as
949 - Bio::PopGen::IO for reading in prettybase (SeattleSNPs)
950 and csv (comma delimited formatted) data.
952 - a directory for implementing population simulations has
953 been added Bio::PopGen::Simulation and 2 simulations - a
954 Coalescent and a simple single-locus multi-allele genetic drift
955 simulation have been provided. This replaces the code in
956 Bio::Tree::RandomTree which has been deprecated until proper
957 methods for generating random phylogenetic trees are
961 - new restrion analysis modules
963 o Bio::Tools::Analysis
964 - web based DNA and Protein analysis framework and several
968 - per residue annotable sequences
971 - Bio::Matrix::PSM - Position Scoring Matrix
972 - Bio::Matrix::IO has been added for generalized parsing of
973 matrix data. Matrix::IO::scoring and Matrix::IO::phylip are
974 initial implementations for parsing BLOSUM/PAM and Phylip
975 Distance matricies respectively. A generic matrix
976 implementation for general use was added in
977 Bio::Matrix::Generic.
984 o Bio::Tools::SiRNA, Bio::SeqFeature::SiRNA
985 - small inhibitory RNA
987 o Bio::SeqFeature::Tools
988 - seqFeature mapping tools
989 - Bio::SeqFeature::Tools::Unflattener.pm
990 -- deal with mapping GenBank feature collections into
991 Chado/GFF3 processable feature sets (with SO term mappings)
993 o Bio::Tools::dpAlign
994 - pure perl dynamic programming sequence alignment
997 o new Bio::SearchIO formats
998 - axt and psl: UCSC formats.
999 - blasttable: NCBI -m 8 or -m 9 format from blastall
1001 o new Bio::SeqIO formats
1002 - chado, tab, kegg, tigr, game
1003 - important fixes for old modules
1007 o improved Bio::Tools::Genewise
1009 o Bio::SeqIO now can recongnize sequence formats automatically from
1012 o new parsers in Bio::Tools:
1013 Blat, Geneid, Lagan, Mdust, Promoterwise, PrositeScan,
1015 o Bio::DB::Registry bugs fixed
1016 - BerkeleyDB-indexed flat files can be used by the OBDA system
1017 - Multiple seqdatabase.ini locations in OBDA_SEARCH_PATH are all
1018 used by the OBDA system
1020 o several new HOWTOs
1021 - SimpleWebAnalysis, Trees, Feature Annotation, OBDA Access, Flat
1024 o hundreds of new and improved files
1028 o Bio::Tree::AlleleNode has been updated to be a container of
1029 an Bio::PopGen::Individual object for use in the Coalescent simulations.
1034 1.2.3 Stable release update
1035 o Bug #1475 - Fix and add speedup to spliced_seq for remote location
1037 o Bug #1477 - Sel --> Sec abbreviation fixed
1038 o Fix bug #1487 where paring in-between locations when
1039 end < start caused the FTLocationFactory logic to fail.
1040 o Fix bug #1489 which was not dealing with keywords as an
1041 arrayref properly (this is fixed on the main trunk because
1042 keywords returns a string and the array is accessible via
1044 o Bio::Tree::Tree memory leak (bug #1480) fixed
1045 Added a new initialization option -nodelete which
1046 won't try and cleanup the containing nodes if this
1048 o Bug with parsing labeled nodes with Bio::TreeIO::newick fixed
1049 this was only present on the branch for the 1.2.1 and 1.2.2 series
1050 - Also merged main trunk changes to the branch which make
1051 newick -> nhx round tripping more effective (storing branch length
1052 and bootstrap values in same locate for NodeNHX and Node
1053 implementations.) Fixes to TreeIO parsing for labeled internal
1054 also required small changes to TreeIO::nhx. Improved
1055 tests for this module as well.
1057 - Fixed bugs in BLAST parsing which couldn't parse NCBI
1058 gapped blast properly (was losing hit significance values due to
1059 the extra unexpeted column).
1060 - Parsing of blastcl3 (netblast from NCBI) now can handle case of
1061 integer overflow (# of letters in nt seq dbs is > MAX_INT)
1062 although doesn't try to correct it - will get the negative
1063 number for you. Added a test for this as well.
1064 - Fixed HMMER parsing bug which prevented parsing when a hmmpfam report
1065 has no top-level family classification scores but does have scores and
1066 alignments for individual domains.
1067 - Parsing FASTA reports where ungapped percent ID is < 10 and the
1068 regular expression to match the line was missing the possibility of
1069 an extra space. This is rare, which is why we probably did not
1071 - BLAST parsing picks up more of the statistics/parameter fields
1072 at the bottom of reports. Still not fully complete.
1073 - SearchIO::Writer::HTMLResultWriter and TextResultWriter
1074 were fixed to include many improvements and added flexiblity
1075 in outputting the files. Bug #1495 was also fixed in the process.
1077 - Update for GFF3 compatibility.
1078 - Added scripts for importing from UCSC and GenBank.
1079 - Added a 1.2003 version number.
1082 - Added a 1.2003 version number.
1083 o SeqIO::swiss Bug #1504 fixed with swiss writing which was not
1084 properly writing keywords out.
1085 o Bio::SeqIO::genbank
1086 - Fixed bug/enhancement #1513 where dates of
1087 the form D-MMM-YYYY were not parsed. Even though this is
1088 invalid format we can handle it - and also cleanup the date
1089 string so it is properly formatted.
1090 - Bug/enhancement #1517 fixed so that SEGMENT line can be parsed
1091 and written with Genbank format. Similarly bug #1515 is fixed to
1092 parse in the ORIGIN text.
1093 o Bio::SeqIO::fasta, a new method called preferred_id_type allows you
1094 to specify the ID type, one of (accession accession.version
1095 display primary). See Bio::SeqIO::preferred_id_type method
1096 documentation for more information.
1097 o Unigene parsing updated to handle file format changes by NCBI
1099 1.2.2 Stable release update
1101 o A series of bug fixes of the Bio::OntologyIO dagflat-related parsers:
1102 - auto-discover ontology name
1103 - bug in parsing relationships when certain characters are in the term
1104 - fixed hard-coded prefix for term identifiers
1105 - various smaller issues
1107 o Fixed bug in Bio::Annotation::OntologyTerm of not implementing all
1108 of Bio::Ontology::TermI
1110 o brought the OBDA Registry code up to latest specs
1114 - accession number retrieval fixed
1116 o Bio::SearchIO::blast - fix bug #1443 (missing last hits), parse megablast
1118 o Bio::SearchIO::Writer::(HTML|Text)ResultWriter fix bugs #1458,
1119 #1459 which now properly report alignment start/end info
1120 for translated BLAST/FASTA searches.
1122 o Bio::TreeIO::newick can parse labeled internal nodes
1124 o Bio::Tools::BPbl2seq can properly report strand info for HSPs
1125 for BLASTX if if you provide -report_type => 'BLASTX' when
1126 initializing a BPbl2seq object. Bioperl 1.3 will have better
1127 support for bl2seq in the SearchIO system.
1129 o Bio::Root::IO support a -noclose boolean flag which will not
1130 close a filehandle upon object cleanup - useful when sharing
1131 a filehandle among objects. Additionally code added s.t.
1132 STDOUT/STDIN/STDERR will never be closed by Root::IO cleanup.
1134 o Bio::Tools::Genemark bug #1435 fixed which was missing last prediction
1136 o Bio::SeqIO::genbank
1137 - bug #1456 fixed which generated extra sequence lines
1138 - write moltype correctly for genpept
1140 1.2.1 Stable release update
1142 o Inclusion of WrapperBase, a needed component for StandAloneBlast
1144 o Addition from main trunk of Ontology objects, principly to allow
1145 BioSQL releases against 1.2.1
1147 o Fixes and cleanup of Bio::Coordinate modules
1149 o A fix to Bio::Index::EMBL allowing retrieval of entries using
1150 the primary accession number
1152 o Other bug fixes, including bpindex GenBank fix
1154 o Bio::SeqIO::genbank bug #1389 fixed
1156 1.2 Stable major release
1158 o More functionality added to Bio::Perl, the newbie module
1160 o Bug fixes in Bio::TreeIO::newick fixes bug introduced in 1.0.2
1161 Support for New Hampshire Extended (NHX) format parsing.
1163 o Bio::Tools added support for parsing Genomewise, Pseudowise, Est2Genome,
1164 Tmhmm, SignalP, Seg, RepeatMasker, FootPrinter, and a lightweight
1167 o New ontology parsing Bio::Ontology
1169 o Bug fixes in Bio::SearchIO for HMMer parsing, support for
1170 multi-report (mlib) fasta reports, support for waba and exonerate.
1172 o Bio::ClusterIO for parsing Unigene clusters
1174 o Bio::Assembly added for representing phrap and ace assembly clusters.
1176 o Rudimentary support for writing Chado XML (see
1177 GMOD project: www.gmod.org for more information)
1179 o Bio::Coordinate for mapping between different coordinate systems such
1180 as protein -> cDNA -> Exon -> DNA and back. Useful for mapping
1181 features into different coordinate systems.
1183 o Bio::DB::GenBank/Bio::DB::GenPept now support Entrez queries
1184 with the get_Stream_by_query method and supports the latest
1185 NCBI eutils interface.
1187 o Bugs fixed in Bio::SeqFeature::Collection an in-memory fast
1188 object for extracting subsets of features : currently only
1189 supports extraction by location.
1191 1.1.1 Developer release
1193 o Deprecated modules are now listed in the DEPRECATED file
1195 o New HowTo documents located in doc/howto describing
1196 a domain of Bioperl.
1198 o Note that bugs are now stored at redmine.open-bio.org/projects/bioperl/
1199 and all old bugs are searchable through the bugzilla interface.
1201 o Several reported bugs in Bio::Tools::Sigcleave and Bio::SimpleAlign
1202 have been addressed.
1204 o Support for Genewise parsing in Bio::Tools::Genewise
1206 o Start of Ontology framework with Bio::Ontology
1208 o Speedup to the Bio::Root::Root object method _rearrange.
1209 A global _load_module method was implemented to simplify the
1210 dynamic loading of modules ala Bio::SeqIO::genbank. This
1211 method is now used by all the XXIO (AlignIO,TreeIO,SearchIO,SeqIO,
1214 o Several performance improvements to sequence parsing in Bio::SeqIO.
1215 Attempt to speedup by reducing object creation overhead.
1217 o Bio::DB::GenBank and Bio::DB::GenPept use the NCBI's approved
1218 method for sequence retrieval with their E-utils CGI scripts.
1219 More work to support Entrez queries to their fullest is planned
1222 o Numerous fixes to Bio::SearchIO and sequence parsing (swissprot)
1224 1.1 Developer release
1226 o Bio::Tools::Run has been broken off into a new pkg bioperl-run,
1227 this separation removes some of the complexity in our test suite
1228 and separates the core modules in bioperl from those that need
1229 external programs to run.
1231 o With latest ExtUtils::MakeMaker module installed SGI/IRIX should
1232 not run into trouble running the makefile
1234 o Bio::Location and Bio::SeqIO::FTHelper are fixed to properly
1235 read,create,and write locations for grouped/split locations
1236 (like mRNA features on genomic sequence).
1238 o Bio::Tools::Phlyo added for wrappers for parsing Molphy (protml)
1239 and PAML (codeml,aaml, etc) parsing.
1241 o Bio::Tree:: objects expanded to handle testing monophyly,
1242 paraphyly, least common ancestor, etc.
1244 o Bio::Coordinate for mapping locations from different coordinate spaces
1246 o Bio::SearchIO::waba added for parsing WABA, Bio::SearchIO::hmmer
1247 added for parsing hmmpfam and hmmsearch output.
1249 o Bio::SearchIO::Writer::TextResultWriter for outputting
1250 a pseudo-blast textfile format
1253 1.0.2 Bug fix release
1255 o Note: The modules Bio::DB::GenBank and Bio::DB::GenPept provided
1256 in this release will not work after December 2002 when NCBI
1257 shuts off the old Entrez cgi scripts. We have already fixed
1258 on our main development branch and the functionality will be
1259 available in the next stable bioperl release (1.2) slated for
1262 o Numerous parsing bugs in Bio::SearchIO::fasta found through
1263 testset by Robin Emig. These were fixed as was the get_aln
1264 method in Bio::Search::HSP::GenericHSP to handle the extra
1265 context sequence that is provided with a FastA alignment.
1267 o Migrating differences between Bio::Search::XX::BlastXX to
1268 Bio::Search::XX::GenericXX objects. This included mechanism
1269 to retrieve whole list of HSPs from Hits and whole list of Hits from
1270 Results in addition to the current next_XX iterator methods that
1271 are available. Added seq_inds() method to GenericHSP which identifies
1272 indexes in the query or hit sequences where conserved,identical,gaps,
1273 or mismatch residues are located (adapted from Steve Chervitz's
1274 implementation in BlastHSP).
1276 o Bio::DB::GFF bugs fixed and are necessary for latest GBrowse release.
1277 Bio::DB::GFF::RelSegment is now Bio::SeqI compliant.
1279 o Bio::Graphics glyph set improved and extended for GBrowse release
1281 o Bio::Tree::Tree get_nodes implementation improvement thanks
1282 to Howard Ross notice performance problem when writing out
1285 o Bio::Location::Fuzzy::new named parameter -loc_type became
1286 -location_type, Bio::Location::Simple::new named parameter
1287 -seqid becamse -seq_id.
1289 o Fixed major Bio::AlignIO::emboss parsing bug on needle output,
1290 was mis-detecting that gaps should be placed at the beginning of
1291 the alignment when the best alignment starts internally in the
1294 1.0.1 Bug fix release
1296 o Minor bug fixes to Bio::DB:GFF. Glyph sets improved.
1298 o Parser fixes in SearchIO blast, fasta for more complete WU BLAST
1299 and mixed (3.3 - 3.4) versions of FASTA.
1301 o Small API change to add methods for completeness across
1302 implementations of Bio::Search objects. These new methods
1303 in the interface are implemented by the GenericXX object as well
1304 as the BlastXX objects.
1305 * Bio::Search::Result::ResultI
1306 - hits() method returns list of all Hits (next_hit is an
1309 * Bio::Search::Hit::HitI
1310 - hsps() method returns list of all HSPs (next_hsp is an
1313 o The Bio::SearchIO::Writer classes have been fixed to handle results
1314 created from either psiblast (Search::BlastXX objects) or
1315 blast|fasta|blastxml objects (Search::GenericXX objects). More work
1316 has to be done here to make it work properly and will nee major
1319 o Bugs in Bio::Tools::HMMER fixed, including
1320 * #1178 - Root::IO destructor wasn't being called
1321 * #1034 - filter_on_cutoff now behaves properly
1323 o Bio::SeqFeature::Computation initialization args fixed and
1326 o Tests are somewhat cleaner, flat.t now properly cleans up after itsself,
1328 o Updated FAQ with more example based answers to typical questions
1330 o Bug #1202 was fixed which would improperly join together qual values
1331 parsed by Bio::SeqIO::qual when a trailing space was not present before
1334 1.0.0 Major Stable Release
1336 This represents a major release of bioperl with significant
1337 improvements over the 0.7.x series of releases.
1339 o Bio::Tools::Blast is officially deprecated. Please see
1340 Bio::SearchIO for BLAST and FastA parsing.
1342 o The methods trunc() and subseq() in Bio::PrimarySeqI now accepts
1343 Bio::LocationI objects as well as start/end.
1345 o Bio::Biblio contains modules for Bibliographic data.
1346 Bio::DB::Biblio contains the query modules. Additionally one can
1347 parse medlinexml from the ebi bibliographic query service (BQS)
1348 system and Pubmed xml from NCBI. See Martin Senger's
1349 documentation in Bio::Biblio for more information.
1351 o Bio::DB::Registry is a sequence database registry part of
1352 Open Bioinformatics Database Access. See
1353 http://obda.open-bio.org for more information.
1355 o File-based and In-Memory Sequence caching is provided by
1356 Bio::DB::InMemoryCache and Bio::DB::FileCache which acts like a
1359 o Bio::Graphics for rendering sequences as PNG,JPG, or GIFs has
1360 been added by Lincoln Stein.
1362 o XEMBL SOAP service access in provided in Bio::DB::XEMBL.
1364 o A FAQ has been started and is included in the release to provide
1365 a starting point for frequent questions and issues.
1367 0.9.3 Developer's release
1369 o Event based parsing system improved (SearchIO). With parsers for
1370 XML Blast (blastxml), Text Blast (blast), and FASTA results (fasta).
1371 Additionally a lazy parsing system for text and html blast reports was
1372 added and is called psiblast (name subject to change in future releases).
1374 o Bio::Search objects improved and standardized with associated Interfaces
1375 written. The concept of a search "Hit" was standardized to be called
1376 "hit" consistently and the use of "subject" was deprecated in all active
1379 o Bio::Structure added (since 0.9.1) for Protein structure objects
1380 and PDB parser to retrieve and write these structures from data files.
1382 o Several important Bio::DB::GFF bug fixes for handling features that
1383 are mapped to multiple reference points. Updated mysql adaptor
1384 so as to be able to store large (>100 megabase) chunks of DNA into
1385 Bio::DB::GFF databases.
1387 0.9.2 Developer's release
1389 o Bio::Search and Bio::SearchIO system introduced for event based
1390 parsing of Blast,Fasta reports Bio::SearchIO supports ncbi BLAST
1391 in text and XML and FASTA reports in standard output format.
1393 o Bio::Tree and Bio::TreeIO for phylogenetic trees. A Random tree
1394 generator is included in Bio::TreeIO::RandomTrees and a
1395 statistics module for evaluating.
1397 o Bio::DB::GFF, Lincoln Stein's GFF database suitable as a DB
1398 server for DAS servers.
1400 o Bio::Tools::BPlite is provides more robust parsing of BLAST
1401 files. The entire BPlite system migrated to using Bio::Root::IO
1402 for the data stream.
1404 o Bio::Tools::Alignment for Consed and sequence Trimming
1407 o Bio::Structure for Protein structure information and parsing
1409 o Bio::DB::GenBank/Bio::DB::GenPept updated to new NCBI Entrez
1410 cgi-bin entry point which should be more reliable.
1412 o Bio::Map and Bio::MapIO for biological map navigation and a
1413 framework afor parsing them in. Only preliminary work here.
1415 o Interface for executing EMBOSS programs locally in Bio::Factory::EMBOSS
1416 Future work will integrate Pise and allow submission of analysis on
1419 o Bio::AnnotationCollectionI and Bio::Annotation::Collection
1420 introduced as new objects for handling Sequence Annotation
1421 information (dblinks, references, etc) and is more robust that
1424 o Bio::Tools::FASTAParser introduced.
1426 o Scripts from the bioperl script submission project and new
1427 scripts from bioperl authors are included in "scripts" directory.
1429 o Factory objects and interfaces are being introduced and are more
1432 o Bio::Root::Root introduced as the base object while
1433 Bio::Root::RootI is now simply an interface.
1435 o Bio::DB::RefSeq provides database access to copy of the NCBI
1436 RefSeq database using the EBI dbfetch script.
1438 0.9.0 Developer's release
1440 o perl version at least 5.005 is now required instead of perl 5.004
1442 o Bio::Tools::Run::RemoteBlast is available for running remote
1445 o Bio::Tools::BPbl2seq was fixed to handle multiple HSPs.
1447 o Bio::SeqFeature::GeneStructure migrated to Bio::SeqFeature::Gene.
1448 Also added are related modules UTR3, UTR5, Exon, Intron,
1449 Promotor, PolyA and Transcript.
1451 o Speedup of translate method in PrimarySeq
1453 o Bio::SimpleAlign has new methods: location_from_column(), slice(),
1454 select(), dot(), get_seq_by_pos(), column_from_residue_number()
1456 o Various fixes to Variation toolkit
1458 o Bio::DB::EMBL provides database access to EMBL sequence data.
1459 Bio::DB::Universal provides a central way to point to indexes
1460 and dbs in a single interface.
1462 o Bio::DB::GFF - a database suitable for running DAS servers locally.
1464 o Bio::Factory::EMBOSS is still in design phase as is
1465 Bio::Factory::ApplicationFactoryI
1467 o Dia models for bioperl design are provided in the models/ directory
1469 0.7.2 Bug fix release
1471 o documentation fixes in many modules - SYNOPSIS code verified
1472 to be runnable in many (but not all modules)
1474 o corrected MANIFEST file from 0.7.1 release
1476 o Bug fix in Bio::SeqIO::FTHelper to properly handle
1479 o Bio::SeqIO::genbank
1480 * Correct parsing and writing of genbank format with protein data
1481 * moltype and molecule separation
1483 o Bio::SeqIO::largefasta fix to avoid inifinite loops
1485 o Bio::SimpleAlign fixed to correctly handle consensus
1486 sequence calculation
1488 o Bio::Tools::HMMER supports hmmer 2.2g
1490 o Bio::Tools::BPlite to support report type specific parsing. Most
1491 major changes are not on the 0.7 branch.
1493 o Bio::Tools::Run::StandAloneBlast exists_blast() fixed and works
1496 o Bio::Variation::AAChange/RNAChange corrected labels and mutated alleles
1497 in several types of mutations:
1498 1.) AA level: deletion, complex
1499 2.) AA level: complex, inframe
1500 3.) RNA level: silent
1502 o BPbl2seq parsing of empty reports will not die, but will return
1503 a valid, empty, Bio::SeqFeature::SimilarityFeature for
1504 $report->query() and $report->subject() methods. So an easy
1505 way to test if report was empty is to see if
1506 $report->query->seqname is undefined.
1508 0.7.1 Bug fix release
1510 o Better parsing of genbank/EMBL files especially fixing bugs
1511 related to Feature table parsing and locations on remote
1512 sequences. Additionally, species name parsing was better.
1514 o Bio::SeqIO::genbank can parse now NCBI produced genbank database
1515 which include a number of header lines.
1517 o More strict genbank and EMBL format writing (corrected number of
1518 spaces where appropriate).
1520 o Bio::Tools::BPlite can better parse BLASTX reports - see BUGS
1521 for related BPlite BUGS that are unresolved in this release.
1523 o Bio::DB::GenBank, Bio::DB::GenPept have less problems
1524 downloading sequences from NCBI via HTTP. Bio::DB::SwissProt can
1525 use expasy mirrors or EBI dbfetch cgi-script.
1527 o A moderate number of documentation improvements were made as
1528 well to provide a better code synopsis in each module.
1531 0.7 Large number of changes, including refactoring of the
1532 Object system, new parsers, new functionality and
1533 all round better system. Highlights are:
1536 o Refactored root of inheritance: moved to a lightweight Bio::Root::RootI;
1537 Bio::Root::IO for I/O and file/handle capabilities.
1539 o Imported BPlite modules from Ian Korf for BLAST
1540 parsing. This is considered the supported BLAST parser;
1541 Bio::Tools::Blast.pm will eventually phase out due to lack of support.
1543 o Improved Sequence Feature model. Added complete location
1544 modelling (with fuzzy and compound locations). See
1545 Bio::LocationI and the modules under Bio/Location. Added
1546 support in Genbank/EMBL format parsing to completely parse
1547 feature tables for complex locations.
1549 o Moved special support for databanks etc to specialized modules under
1550 Bio/Seq/. One of these supports very large sequences through
1551 a temporary file as a backend.
1553 o Explicit Gene, Transcript and Exon SeqFeature objects, supporting
1554 CDS retrieval and exon shuffling.
1556 o More parsers: Sim4, Genscan, MZEF, ESTScan, BPbl2seq, GFF
1558 o Refactored Bio/DB/GenBank+GenPept. There is now also DB/SwissProt and
1559 DB/GDB (the latter has platform-specific limitations).
1561 o New analysis parser framework for HT sequence annotation (see
1562 Bio::SeqAnalysisParserI and Bio::Factory::SeqAnalysisParserFactory)
1564 o New Alignment IO framework
1566 o New Index modules (Swissprot)
1568 o New modules for running Blast within perl
1569 (Bio::Tools::Run::StandAloneBlast). Added modules for running
1570 Multiple Sequence Alignment tools ClustalW and TCoffee
1571 (Bio::Tools::Run::Alignment).
1573 o New Cookbook-style tutorial (see bptutorial.pl). Improved
1574 documentation across the package.
1576 o Much improved cross platform support. Many known incompatibilities
1577 have been fixed; however, NT and Mac do not work across the entire
1578 setup (see PLATFORMS).
1580 o Many bug fixes, code restructuring, etc. Overall stability and
1581 maintainability benefit a lot.
1583 o A total of 957 automatic tests
1588 There are very few functionality changes but a large
1589 number of software improvements/bug fixes across the package.
1591 o The EMBL/GenBank parsing are improved.
1593 o The Swissprot reading is improved. Swissprot writing
1594 is disabled as it doesn't work at all. This needs to
1595 wait for 0.7 release
1597 o BLAST reports with no hits are correctly parsed.
1599 o Several other bugs of the BLAST parser (regular expressions, ...)
1602 o Old syntax calls have been replaced with more modern syntax
1604 o Modules that did not work at all, in particular the Sim4
1605 set have been removed
1607 o Bio::SeqFeature::Generic and Bio::SeqFeature::FeaturePair
1608 have improved compliance with interface specs and documentation
1610 o Mailing list documentation updated throughout the distribution
1612 o Most minor bug fixes have happened.
1614 o The scripts in /examples now work and have the modern syntax
1615 rather than the deprecated syntax
1618 0.6.1 Sun April 2 2000
1620 o Sequences can have Sequence Features attached to them
1621 - The sequence features can be read from or written to
1622 EMBL and GenBank style flat files
1624 o Objects for Annotation, including References (but not
1625 full medline abstracts), Database links and Comments are
1628 o A Species object to represent nodes on a taxonomy tree
1631 o The ability to parse HMMER and Sim4 output has been added
1633 o The Blast parsing has been improved, with better PSI-BLAST
1634 support and better overall behaviour.
1636 o Flat file indexed databases provide both random access
1637 and sequential access to their component sequences.
1639 o A CodonTable object has been written with all known
1640 CodonTables accessible.
1642 o A number of new lightweight analysis tools have been
1643 added, such as molecular weight determination.
1645 The 0.6 release also has improved software engineering
1647 o The sequence objects have been rewritten, providing more
1648 maintainable and easier to implement objects. These
1649 objects are backwardly compatible with the 0.05.1 objects
1651 o Many objects are defined in terms of interfaces and then
1652 a Perl implementation has been provided. The interfaces
1653 are found in the 'I' files (module names ending in 'I').
1655 This means that it is possible to wrap C/CORBA/SQL access
1656 as true "bioperl" objects, compatible with the rest of
1659 o The SeqIO system has been overhauled to provide better
1660 processing and perl-like automatic interpretation of <>
1663 o Many more tests have been added (a total of 172 automatic
1664 tests are now run before release).
1668 0.05.1 Tue Jun 29 05:30:44 1999
1669 - Central distribution now requires Perl 5.004. This was
1670 done to get around 5.003-based problems in Bio/Index/*
1672 - Various bug fixes in the Bio::Tools::Blast modules
1673 including better exception handling and PSI-Blast
1674 support. See Bio/Tools/Blast/CHANGES for more.
1675 - Fixed the Parse mechanism in Seq.pm to use readseq.
1676 Follow the instructions in README for how to install
1677 it (basically, you have to edit Parse.pm).
1678 - Improved documentation of Seq.pm, indicating where
1679 objects are returned and where strings are returned.
1680 - Fixed uninitialized warnings in Bio::Root::Object.pm
1681 and Bio::Tools::SeqPattern.pm.
1682 - Bug fixes for PR#s: 30,31,33-35,41,42,44,45,47-50,52.
1684 0.05 Sun Apr 25 01:14:11 1999
1685 - Bio::Tools::Blast modules have less memory problems
1686 and faster parsing. Webblast uses LWP and supports
1687 more functionality. See Bio/Tools/Blast/CHANGES for more.
1688 - The Bio::SeqIO system has been started, moving the
1689 sequence reformatting code out of the sequence object
1690 - The Bio::Index:: system has been started, providing
1691 generic index capabilities and specifically works for
1692 Fasta formatted databases and EMBL .dat formatted
1694 - The Bio::DB:: system started, providing access to
1695 databases, both via flat file + index (see above) and
1697 - The scripts/ directory, where industrial strength scripts
1698 are put has been started.
1699 - Many changes - a better distribution all round.
1701 0.04.4 Wed Feb 17 02:20:13 1999
1702 - Bug fixes in the Bio::Tools::Blast modules and postclient.pl
1703 (see Bio::Tools::Blast::CHANGES).
1704 - Fixed a bug in Bio::Tools::Fasta::num_seqs().
1705 - Beefed up the t/Fasta.t test script.
1706 - Small fix in Bio::Seq::type() (now always returns a string).
1707 - Changed Bio::Root::Utilities::get_newline_char() to
1708 get_newline() since it could return more than one char.
1709 - Added $NEWLINE and $TIMEOUT_SECS to Bio::Root::Global.
1710 - Changed default timeout to 20 seconds (was 3).
1711 - Moved lengthy modification notes to the bottom of some files.
1712 - Fixed SimpleAlign write_fasta bug.
1713 - Beefed up SimpleAlign.t test
1715 0.04.3 Thu Feb 4 07:48:53 1999
1716 - Bio::Root::Object.pm and Global.pm now detect when
1717 script is run as a CGI and suppress output that is only
1718 appropriate when running interactively.
1719 - Bio::Root::Err::_set_context() adds name of script ($0).
1720 - Added comments in Bio::Tools::WWW.pm and Bio::Root::Utilities.pm
1721 regarding the use of the static objects via the qw(:obj) tag.
1722 - Fixed the ambiguous reverse calls in Seq.pm and UnivAln.pm to
1723 CORE::reverse, avoiding Perl warnings.
1724 - Bug fixes in Bio::Tools::Blast modules (version 0.074) and
1725 example scripts (see Bio::Tools::Blast::CHANGES).
1726 - examples/seq/seqtools.pl no longer always warns about using
1727 -prot or -nucl command-line arguments; only when using the
1729 - Methods added to Bio::Root::Utilities: create_filehandle(),
1730 get_newline_char(), and taste_file() to generalize filehandle
1731 creation and autodetect newline characters in files/streams
1732 (see bug report #19).
1733 - Bio::Root::IOManager::read() now handles timeouts and uses
1734 Utilities::create_filehandle().
1735 - Bio::Tools::Fasta.pm uses Utilities::get_newline_char() instead
1736 of hardwiring in "\n".
1737 - Bug fixes in the Bio::SimpleAlign and Bio::Tools::pSW
1739 0.04.2 Wed Dec 30 02:27:36 1998
1740 - Bug fixes in Bio::Tools::Blast modules, version 0.073
1741 (see Bio::Tools::Blast::CHANGES).
1742 - Changed reverse calls in Bio/Seq.pm and Bio/UnivAln.pm
1743 to CORE::reverse (prevents ambiguous warnings with 5.005).
1744 - Appending '.tmp.bioperl' to temporary files created by
1745 Bio::Root::Utilities::compress() or uncompress() to
1746 make it easy to identify & cleanup these files as needed.
1747 - Developers: Created CVS branch release-0-04-bug from
1748 release-0-04-1. Before making bug fixes to the 0.04.1 release,
1749 be sure to cvs checkout this branch into a clean area.
1751 0.04.1 Wed Dec 16 05:39:15 1998
1752 - Bug fixes in Bio::Tools::Blast modules, version 0.072
1753 (see Bio::Tools::Blast::CHANGES).
1754 - Compile/SW/Makefile.PL now removes *.o and *.a files
1757 0.04 Tue Dec 8 07:49:19 1998
1758 - Lots of new modules added including:
1759 * Ewan Birney's Bio::SimpleAlign.pm, Bio::Tools::AlignFactory.pm,
1760 and Bio/Compile directory containing XS-linked C code for
1761 creating Smith-Waterman sequence alignments from within Perl.
1762 * Steve Chervitz's Blast distribution has been incorporated.
1763 * Georg Fuellen's Bio::UnivAln.pm for multiple alignment objects.
1764 - Bio/examples directory for demo scripts for all included modules.
1765 - Bio/t directory containing test suit for all included modules.
1766 - For changes specific to the Blast-related modules prior to
1767 incorporation in this central distribution, see the CHANGES
1768 file in the Bio/Tools/Blast directory.
1770 0.01 Tue Sep 8 14:23:22 1998
1771 - original version from central CVS tree; created by h2xs 1.18