bioperl bioperl-run issues

bioperl / bioperl-run

BioPerl wrappers

http://bioperl.org

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issues

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t/SABlastPlus.t failures with makeblastdb from ncbi-blast+ 2.16.0

#62 emollier opened 3 months ago
0
Updating Mauricio's email

#61 arareko closed 4 years ago
0
Where to acquire Helicobacter_pylori.mod needed by t/Genemark.hmm.prokaryotic.t ?

#60 mr-c opened 4 years ago
0
Bug in Eponine test

#59 dionys opened 5 years ago
0
BEDTools issues

#58 cjfields opened 5 years ago
0
Build.PL mentions `Bio::Run` that does not exist

#57 carandraug opened 5 years ago
2
Perl

#56 AmitaCM closed 6 years ago
1
Issue with Bowtie in test suite

#55 tillea opened 6 years ago
1
adjust version regex with optional space for BlastPlus

#54 dmr3 closed 5 years ago
1
bug in Bio::Tools::Run::Alignment::StandAloneFasta

#53 cjfields opened 7 years ago
0
Test with latest bowtie is failing

#52 tillea opened 7 years ago
0
SABlastPlus tests fail with latest version of BLAST+

#51 cjfields opened 7 years ago
0
qualifiers for for water/needle@ Bio::Factory::EMBOSS

#50 rafalcode closed 7 years ago
5
Update Phyml.pm

#49 qifei9 opened 7 years ago
0
Bio::Tools::Run::StandAloneBlastPlus HTML output

#48 bretonics closed 7 years ago
4
'cpgplot' input sequence not recognized

#47 piatekmj opened 7 years ago
9
Bio::Factory::EMBOSS dies on OSX when checking for operating system

#46 piatekmj closed 7 years ago
5
infernal does not contan cmscore since version 1.1

#45 tillea opened 7 years ago
1
Bio::Tools::Run::Phylo::Phyml, rand_starts cannot be set to 0

#44 qifei9 closed 7 years ago
1
Bio::Tools::Run::Phylo::Phyml use default parameter for interleaved input, but it use sequential input

#43 qifei9 closed 7 years ago
1
Wrapper for ExaML phylogenetic inference added

#42 hettling opened 8 years ago
1
Index on cpanm?

#41 keiranmraine opened 8 years ago
1
adding support for RAxML's rapid bootstrap

#40 hettling closed 8 years ago
0
Making Raxml test run

#39 hettling closed 8 years ago
0
Adding support for RaXMLs fast bootstrap option (-a)

#38 hettling closed 8 years ago
0
DB can't be found

#37 ksteczk opened 8 years ago
1
problem in Installing Bio::Seq, Bio::DB::GFF,

#36 amoltej opened 8 years ago
6
Codeml (v 4v4d) using fixed kappa value, reports wrong kappa

#35 cjfields closed 7 years ago
3
Bio::Tools::Run::StandAloneBlastPlus --remote database with '/' separator

#34 cjfields opened 9 years ago
1
Bio::Tools::Run::Phylo::Phyml, tree_string

#33 cjfields opened 9 years ago
0
Undocumented need for Array::Compare.

#32 cjfields opened 9 years ago
2
Bio::Tools::Run::Phylo::Phyml Lacks LG model of AA sequence evolution

#31 cjfields opened 9 years ago
0
version() not implemented for Bio::Tools::Run::StandAloneBlastPlus

#30 cjfields opened 9 years ago
0
Bio::Tools::Run::StandAloneBlastPlus tests failing with latest BLAST+

#29 cjfields opened 9 years ago
3
Bio::Tools::Run::BWA failing tests

#28 cjfields opened 9 years ago
0
Bio::Tools::Run::Phylo::Phyml -- documented values for -f parameter

#27 cjfields opened 9 years ago
0
Bio::Tools::Run::Phylo::Phyml -- Bootstrap and other confidence measures

#26 cjfields opened 9 years ago
0
Bio::Tools::Run::StandAloneBlastPlus "entrez_query" option

#25 cjfields opened 9 years ago
3
bioperl-run LVB.pm and LVB.t require updates for LVB version 2.3

#24 cjfields opened 9 years ago
2
-task blastn option is not available in Bio::Tools::Run::StandAloneBlastPlus

#23 cjfields opened 9 years ago
0
Bio::Tools::Run::Alignment::MAFFT: not able to specify alignment run parameters

#22 cjfields opened 9 years ago
1
Bio::Tools::Run::Genewise doesn't accept parameters as described in its documentation

#21 cjfields opened 9 years ago
0
Bio::Tools::Run::Primer3 has not updated for Primer3 versions 2 and above

#20 cjfields opened 9 years ago
3
ecoli.nt not available from ftp://ncbi.nlm.nih.gov, causes t/Tools/Run/StandaloneBlast.t to fail

#19 cjfields opened 9 years ago
1
Add Amap, Kalign and Probcon Quiet option

#18 cjfields opened 9 years ago
2
mumsa wrapper

#17 cjfields opened 9 years ago
1
Implement a seqgen wrapper in bioperl-run

#16 cjfields opened 9 years ago
1
Supply TEMPLATE and SUFFIX for temporary query sequence files.

#15 ghost closed 9 years ago
0
Wrappers for ExaML, ExaBayes, *BEAST

#14 rvosa opened 9 years ago
2
Raxml module did not pass test and -w option only worked with cwd

#13 hettling closed 9 years ago
2