Joachim Bargsten > Bio-Gonzales-0.053

Bio-Gonzales-0.053

This Release Bio-Gonzales-0.053  [Download] [Browse 26 Nov 2013
Latest Release Bio-Gonzales-0.0547  [Download] [Browse 05 May 2014
Latest Dev. Release Bio-Gonzales-0.0547_01  [Download] [Browse 17 May 2014
Other Releases
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CPAN Testers PASS (298)   FAIL (8)   NA (5)   [ View Reports ] [ Perl/Platform Version Matrix ]
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License The Perl 5 License (Artistic 1 & GPL 1)
Special Files
Build.PL
Changes
LICENSE
MANIFEST
META.yml
README

Modules

Bio::Gonzales Speedy functions to manipulate biological data     0.03
Bio::Gonzales::Align     0.0101
Bio::Gonzales::Align::ConsensePrimer     0.0101
Bio::Gonzales::Align::ConsensePrimer1     0.0101
Bio::Gonzales::Align::IO     0.0101
Bio::Gonzales::Align::IO::MAF     0.0101
Bio::Gonzales::Align::IO::Stockholm IO class for the stockholm format     0.0101
Bio::Gonzales::Align::Jalview     0.0101
Bio::Gonzales::Assembly::IO assembly related stuff     0.0101
Bio::Gonzales::Domain::Group     0.0101
Bio::Gonzales::Domain::Identification::HMMER     0.0101
Bio::Gonzales::Feat a sequence feature     0.0101
Bio::Gonzales::Feat::IO     0.0101
Bio::Gonzales::Feat::IO::BED     0.0101
Bio::Gonzales::Feat::IO::Base     0.0101
Bio::Gonzales::Feat::IO::GFF3 read and write gff files     0.0101
Bio::Gonzales::Feat::IO::SWISS     0.0101
Bio::Gonzales::Graphics::BLAST make your blast result nice     0.0101
Bio::Gonzales::Graphics::Glyph::colorfulBox      
Bio::Gonzales::IDMapIO remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO     0.0101
Bio::Gonzales::Matrix::IO Library for simple matrix IO     0.0101
Bio::Gonzales::Matrix::IO::csv     0.0101
Bio::Gonzales::Matrix::Util     0.0101
Bio::Gonzales::MiniFeat     0.0101
Bio::Gonzales::Phylo::Dendroscope Color phylogenetic trees in Dendroscope format     0.0101
Bio::Gonzales::Phylo::IO     0.0101
Bio::Gonzales::Phylo::Util utility functions for phylogenetic analysis     0.0101
Bio::Gonzales::PrimarySeqIX     0.0101
Bio::Gonzales::Project     0.0101
Bio::Gonzales::Range::Cluster cluster sorted ranges iteratively     0.0101
Bio::Gonzales::Range::GroupedOverlap cluster overlapping ranges that are in the same group     0.0101
Bio::Gonzales::Range::Overlap find overlapping ranges     0.0101
Bio::Gonzales::Range::Util     0.0101
Bio::Gonzales::Role::BioPerl::Constructor     0.0101
Bio::Gonzales::Search::IO::BLAST     0.0101
Bio::Gonzales::Search::IO::HMMER3     0.0101
Bio::Gonzales::Seq Gonzales Seqeuence Object     0.0101
Bio::Gonzales::Seq::Filter filter sequence data     0.0101
Bio::Gonzales::Seq::Filter::DuplicateSeqs     0.0101
Bio::Gonzales::Seq::Filter::ProteinCleaner clean protein sequences     0.0101
Bio::Gonzales::Seq::IO fast utility functions for sequence IO     0.0101
Bio::Gonzales::Seq::IO::Fasta     0.0101
Bio::Gonzales::Seq::IO::fastq     0.0101
Bio::Gonzales::Seq::LongestTranscript     0.0101
Bio::Gonzales::Seq::Util     0.0101
Bio::Gonzales::Seq::Validate::fasta     0.0101
Bio::Gonzales::Tools::SeqMask     0.0101
Bio::Gonzales::Tools::SeqStats     0.0101
Bio::Gonzales::Util Utility functions for common tasks     0.03
Bio::Gonzales::Util::Cerial convenience functions for yaml storage     0.01
Bio::Gonzales::Util::Development functions handy for general development     0.0202
Bio::Gonzales::Util::Development::File Helper functions for all filesystem related tasks     0.0202
Bio::Gonzales::Util::Development::Module functions handy for module development     0.0202
Bio::Gonzales::Util::File Utility functions for file stuff     0.0101
Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER::SeqMarks     0.0101
Bio::Gonzales::Util::Graphics::Color::Generator     0.0202
Bio::Gonzales::Util::IO::Compressed      
Bio::Gonzales::Util::Log     0.0101
Bio::Gonzales::Util::Math     0.0101
Bio::Gonzales::Util::Math::kNN::via::Distances Calculate kNN clusterings from already calculated distances     0.0101
Bio::Gonzales::Util::Role::FileIO     0.0101
Bio::Gonzales::Util::Text text and string functions     0.01
Bio::Gonzales::Util::YAML convenience functions for yaml storage     0.01
Bio::Matrix::IO::mcl     0.0101

Documentation

BaMo::Role::FileIO File input & ouput interface for parser classes  
Bio::Gonzales::AV analysis project utils  
Bio::Gonzales::Align::Util Utility functions for aligment stuff  
Bio::Gonzales::Util::Common::Visual::Color::Generator generate distinguishable colors in RGB format  
Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER Identify Protein Domains with HMMER  
Bio::Gonzales::Util::Math::Util  
aln2aln convert different alignment formats to another alignment format  
bin/gffcds2seq.pl  
coords2gff.pl convert mummer coords files to gff3 format  
fadiff diff fasta files  
fafind-eq-seq find equal sequences  
fasta-grep grep fasta files  
show-align2clustalw.pl convert mummer alignment files to clustalw format