Kwalitee Issues


Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.


Fix the version(s).


Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: Bio::PanGenome::Exceptions


Add a META.json to the distribution. Your buildtool should be able to autogenerate it.


If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.


Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::PanGenome::Exceptions


Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.


Name Abstract Version View
Bio::PanGenome Create a pan genome metacpan
Bio::PanGenome::AnalyseGroups Take in a groups file and the original FASTA files and create plots and stats metacpan
Bio::PanGenome::AnnotateGroups Take in a group file and assosiated GFF files for the isolates and update the group name to the gene name metacpan
Bio::PanGenome::ChunkFastaFile Take in a FASTA file and chunk it up into smaller pieces. metacpan
Bio::PanGenome::ClustersRole A role to read a clusters file from CD hit metacpan
Bio::PanGenome::CombinedProteome Take in multiple FASTA sequences containing proteomes and concat them together and output a FASTA file, filtering out more than 5% X's metacpan
Bio::PanGenome::CommandLine::CreatePanGenome Take in FASTA files of proteins and cluster them metacpan
Bio::PanGenome::CommandLine::ExtractProteomeFromGff Take in GFF files and output the proteome metacpan
Bio::PanGenome::CommandLine::PanGenomePostAnalysis Perform the post analysis on the pan genome metacpan
Bio::PanGenome::CommandLine::PanGenomeReorderSpreadsheet Take in a tree and a spreadsheet and output a reordered spreadsheet metacpan
Bio::PanGenome::CommandLine::ParallelAllAgainstAllBlastp Take in a FASTA file of proteins and blast against itself metacpan
Bio::PanGenome::CommandLine::PlotPanGenomeGroups Take in the groups file and output some summary plots metacpan
Bio::PanGenome::CommandLine::QueryPanGenome Take in a groups file and the protein fasta files and output selected data metacpan
Bio::PanGenome::CommandLine::TransferAnnotationToGroups Take in a groups file and a set of GFF files and transfer the consensus annotation metacpan
Bio::PanGenome::Exceptions Exceptions for input data metacpan
Bio::PanGenome::External::Blastp Wrapper around NCBIs blastp command metacpan
Bio::PanGenome::External::Cdhit Wrapper to run cd-hit metacpan
Bio::PanGenome::External::Makeblastdb Wrapper around NCBIs makeblastdb command metacpan
Bio::PanGenome::External::Mcl Wrapper around MCL which takes in blast results and outputs clustered results metacpan
Bio::PanGenome::External::Muscle Wrapper around Muscle for sequence alignment metacpan
Bio::PanGenome::External::PostAnalysis Perform the post analysis metacpan
Bio::PanGenome::External::Segmasker Wrapper around Segmasker for low complexity filtering metacpan
Bio::PanGenome::ExtractProteomeFromGFF Take in a GFF file and create protein sequences in FASTA format metacpan
Bio::PanGenome::ExtractProteomeFromGFFs Take in GFF files and create protein sequences in FASTA format metacpan
Bio::PanGenome::FilterFullClusters Take an a clusters file from CD-hit and the fasta file and output a fasta file without full clusters metacpan
Bio::PanGenome::FilterUnknownsFromFasta Take in fasta files, remove sequences with too many unknowns and return a list of the new files metacpan
Bio::PanGenome::GeneNamesFromGFF Parse a GFF and efficiently extract ID -> Gene Name metacpan
Bio::PanGenome::GroupLabels Add labels to the groups metacpan
Bio::PanGenome::GroupStatistics Add labels to the groups metacpan
Bio::PanGenome::InflateClusters Take the clusters file from cd-hit and use it to inflate the output of MCL metacpan
Bio::PanGenome::JobRunner::LSF Execute a set of commands using LSF metacpan
Bio::PanGenome::JobRunner::Local Execute a set of commands locally metacpan
Bio::PanGenome::JobRunner::Role A role to add job runner functionality metacpan
Bio::PanGenome::Output::DifferenceBetweenSets Given two sets of isolates and a group file, output whats unique in each and whats in common metacpan
Bio::PanGenome::Output::GroupMultifasta Take in a group and create a multifasta file metacpan
Bio::PanGenome::Output::GroupTabFiles Take in an array of files and output raw tab files for analysis by R to turn into plots metacpan
Bio::PanGenome::Output::GroupsMultifastaNucleotide Take in a GFF files and a groups file and output one multifasta file per group with nucleotide sequences. metacpan
Bio::PanGenome::Output::GroupsMultifastas Take in a list of groups and create multifastas files for each group metacpan
Bio::PanGenome::Output::GroupsMultifastasNucleotide Take in a set of GFF files and a groups file and output one multifasta file per group with nucleotide sequences. metacpan
Bio::PanGenome::Output::NumberOfGroups Create raw output files of group counts for turning into plots metacpan
Bio::PanGenome::Output::OneGenePerGroupFasta Output a fasta file with one gene per group metacpan
Bio::PanGenome::Output::QueryGroups Output the groups of the union of a set of input isolates metacpan
Bio::PanGenome::ParallelAllAgainstAllBlast Run all against all blast in parallel metacpan
Bio::PanGenome::Plot::FreqOfGenes Take in an array of frequencies of groups and output a plot metacpan
Bio::PanGenome::PostAnalysis Post analysis of pan genomes metacpan
Bio::PanGenome::PrepareInputFiles Take in a mixture of FASTA and GFF input files and output FASTA proteomes only metacpan
Bio::PanGenome::ReorderSpreadsheet Take in a tree file and a spreadsheet and output a spreadsheet with reordered columns metacpan
Bio::PanGenome::SampleOrder Take in a tree file and return an ordering of the samples metacpan
Bio::PanGenome::SequenceLengths Take in a fasta file and create a hash with the length of each sequence metacpan

Other Files

MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan metacpan
dist.ini metacpan