Joachim Bargsten > Bio-Gonzales

Bio-Gonzales

This Release Bio-Gonzales-0.062  [Download] [Browse 16 Sep 2016
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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     0.062
Bio::Gonzales::Align     0.062
Bio::Gonzales::Align::ConsensePrimer     0.062
Bio::Gonzales::Align::ConsensePrimer1     0.062
Bio::Gonzales::Align::IO     0.062
Bio::Gonzales::Align::IO::MAF     0.062
Bio::Gonzales::Align::IO::Stockholm IO class for the stockholm format     0.062
Bio::Gonzales::Align::Jalview     0.062
Bio::Gonzales::Assembly::IO assembly related stuff     0.062
Bio::Gonzales::Domain::Group     0.062
Bio::Gonzales::Domain::Identification::HMMER     0.062
Bio::Gonzales::Feat a sequence feature     0.062
Bio::Gonzales::Feat::IO     0.062
Bio::Gonzales::Feat::IO::BED     0.062
Bio::Gonzales::Feat::IO::Base     0.062
Bio::Gonzales::Feat::IO::CDhit     0.062
Bio::Gonzales::Feat::IO::GFF3 read and write gff files     0.062
Bio::Gonzales::Feat::IO::MUM     0.062
Bio::Gonzales::Feat::IO::SWISS     0.062
Bio::Gonzales::GO::Util     0.062
Bio::Gonzales::Graphics::BLAST make your blast result nice     0.062
Bio::Gonzales::Graphics::Glyph::colorfulBox     0.062
Bio::Gonzales::IDMapIO remap ids of 'objects', should be used in IO-classes, like Bio::SeqIO     0.062
Bio::Gonzales::Matrix::IO Library for simple matrix IO     0.062
Bio::Gonzales::Matrix::IO::csv     0.062
Bio::Gonzales::Matrix::Util     0.062
Bio::Gonzales::MiniFeat     0.062
Bio::Gonzales::Phylo::Dendroscope Color phylogenetic trees in Dendroscope format     0.062
Bio::Gonzales::Phylo::IO     0.062
Bio::Gonzales::Phylo::Util utility functions for phylogenetic analysis     0.062
Bio::Gonzales::PrimarySeqIX     0.062
Bio::Gonzales::Project     0.062
Bio::Gonzales::Project::Functions organize your computational experiments     0.062
Bio::Gonzales::Range::Cluster cluster sorted ranges iteratively     0.062
Bio::Gonzales::Range::GroupedOverlap cluster overlapping ranges that are in the same group     0.062
Bio::Gonzales::Range::Overlap find overlapping ranges     0.062
Bio::Gonzales::Range::Util     0.062
Bio::Gonzales::Role::BioPerl::Constructor     0.062
Bio::Gonzales::Search::IO::BLAST     0.062
Bio::Gonzales::Search::IO::HMMER3     0.062
Bio::Gonzales::Seq Gonzales Sequence Object     0.062
Bio::Gonzales::Seq::Filter filter sequence data     0.062
Bio::Gonzales::Seq::Filter::DuplicateSeqs     0.062
Bio::Gonzales::Seq::Filter::ProteinCleaner clean protein sequences     0.062
Bio::Gonzales::Seq::IO fast utility functions for sequence IO     0.062
Bio::Gonzales::Seq::IO::Fasta     0.062
Bio::Gonzales::Seq::IO::fastq     0.062
Bio::Gonzales::Seq::LongestTranscript     0.062
Bio::Gonzales::Seq::Util     0.062
Bio::Gonzales::Seq::Validate::fasta     0.062
Bio::Gonzales::Stat::Util     0.062
Bio::Gonzales::String::Util     0.0101
Bio::Gonzales::Tools::SeqMask     0.062
Bio::Gonzales::Tools::SeqStats     0.062
Bio::Gonzales::Util Utility functions for common tasks     0.062
Bio::Gonzales::Util::Cerial convenience functions for yaml and json IO     0.062
Bio::Gonzales::Util::Development functions handy for general development     0.062
Bio::Gonzales::Util::Development::File Helper functions for all filesystem related tasks     0.062
Bio::Gonzales::Util::Development::Module functions handy for module development     0.062
Bio::Gonzales::Util::File Utility functions for file stuff     0.062
Bio::Gonzales::Util::FunCon::Domains::Identification::HMMER::SeqMarks     0.062
Bio::Gonzales::Util::Graphics::Color::Generator     0.062
Bio::Gonzales::Util::IO::Compressed      
Bio::Gonzales::Util::Log basic logging for Bio::Gonzales     0.062
Bio::Gonzales::Util::Math     0.062
Bio::Gonzales::Util::Math::kNN::via::Distances Calculate kNN clusterings from already calculated distances     0.062
Bio::Gonzales::Util::Role::FileIO     0.062
Bio::Gonzales::Util::Text text and string functions     0.062
Bio::Gonzales::Var::IO::VCF parse VCF files     0.0101
Bio::Gonzales::Var::Util     0.0101
Bio::Matrix::IO::mcl     0.062

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  
bg_fasplit.pl split sequences in fasta files by given regular expression  
bg_fastat.pl fasta file statistics  
bg_xlsx2tsv convert xlsx files to tsv format  
bin/gffcds2seq.pl  
bin/ppt_watch_process.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  
gonz_unmap.pl unmap or remap identifiers/strings using a given id mapping  
m2x matrix (CSV) data to xlsx format  
ppt_profile_cmd.pl track the cpu and memory usage of a command  
show-align2clustalw.pl convert mummer alignment files to clustalw format