bioperl-run
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bioperl
BioPerl wrappers
--- Author Name: **Chris Fields** (@cjfields) Original Redmine Issue: 3213, https://redmine.open-bio.org/issues/3213 Original Date: 2011-04-20 Original Assignee: Bioperl Guts --- Indexing of BLAST databases using `makeblastdb` with BLAST+ 2.2.24+ and up...
--- Author Name: **Chris Fields** (@cjfields) Original Redmine Issue: 3210, https://redmine.open-bio.org/issues/3210 Original Date: 2011-04-19 Original Assignee: Bioperl Guts --- I have TODO’d the assembly pipeline tests for t/BWA.t in bioperl-run...
--- Author Name: **Adam Retchless** (Adam Retchless) Original Redmine Issue: 3202, https://redmine.open-bio.org/issues/3202 Original Date: 2011-04-13 Original Assignee: Bioperl Guts --- In the documentation, the values for the “frequencies” parameters disagree...
--- Author Name: **Adam Retchless** (Adam Retchless) Original Redmine Issue: 3201, https://redmine.open-bio.org/issues/3201 Original Date: 2011-04-13 Original Assignee: Bioperl Guts --- The documentation for the Phyml wrapper does not describe how...
--- Author Name: **Remi empty** (Remi empty) Original Redmine Issue: 3150, https://redmine.open-bio.org/issues/3150 Original Date: 2010-10-27 Original Assignee: Bioperl Guts --- When running this code: my $fac = Bio::Tools::Run::StandAloneBlastPlus->new( -db_name =>...
--- Author Name: **Daniel Barker** (Daniel Barker) Original Redmine Issue: 3125, https://redmine.open-bio.org/issues/3125 Original Date: 2010-07-28 Original Assignee: Bioperl Guts --- The user interface to LVB has changed. From LVB 2.3,...
--- Author Name: **Peng Yu** (Peng Yu) Original Redmine Issue: 3097, https://redmine.open-bio.org/issues/3097 Original Date: 2010-06-09 Original Assignee: Bioperl Guts --- Anyway, I restate my original problem below. bioperl’s bl2seq by...
--- Author Name: **Oliver Niehuis** (Oliver Niehuis) Original Redmine Issue: 3075, https://redmine.open-bio.org/issues/3075 Original Date: 2010-05-10 Original Assignee: Bioperl Guts --- Hi, this is request to update the Bio::Tools::Run::Alignment::MAFFT module. I...
--- Author Name: **Dave Messina** (@DaveMessina) Original Redmine Issue: 3072, https://redmine.open-bio.org/issues/3072 Original Date: 2010-05-02 Original Assignee: Bioperl Guts --- I’m pasting my email pretty much verbatim below, but here’s a...
--- Author Name: **John MC** (John MC) Original Redmine Issue: 3056, https://redmine.open-bio.org/issues/3056 Original Date: 2010-04-12 Original Assignee: Bioperl Guts --- Bio::Tools::Run::Primer3 relies on the list of Primer3 1.X arguments hardcoded...