What is BioPerl?

BioPerl is a toolkit of perl modules useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl.

Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as CVS modules in our repository.

Current modules of BioPerl:

• bioperl::live - Core BioPerl 1.x code
• p5::bpwrapper - BioPerl scripts and utilities
• Bio::EUtilities - Low-level OO Perl interface for NCBI's eutils
• Bio::DB::Taxonomy::sqlite
• Bio::FeatureIO - Sequence Feature streams
• Bio::DB::SeqFeature
• Bio::DB::GFF
• Bio::Variation
• Bio::DB::RefSeq
• Bio::DB::NCBIHelper - BioPerl modules for accessing data from NCBI
• Bio::DB::SwissProt -
• Bio::Procedural - Procedural interface to a subset of the BioPerl functionality
• Bio::DB::HIV - BioPerl interface to the Los Alamos HIV Sequence Database
• Bio::Restriction - BioPerl distribution for restriction enzymes
• Bio::DB::EMBL - BioPerl modules for accessing data from EMBL-EBI
• Bio::DB::BioFetch
• bioperl::pipeline - Analysis pipelines from wrappers
• bioperl::run - BioPerl wrappers
• Bio::Symbol
• Bio::Tools::Run-* - Run wrapper for some Bio assembler code.
• Bio::ASN1::EntrezGene - ASN1 parser for EntrezGene data
• Bio::SeqIO::lasergene
• Bio::Tools::Run::Alignment::Clustalw
• Bio::Tools::Phylo::PAML - bioperl interface to PAML (Phylogenetic Analysis by Maximum Likelihood)
• Bio::Cluster
• bioperl::docker - Docker files for BioPerl
• Bio::Map
• Bio::DB::Ace - Bioperl distribution to interface to ACeDB servers
• Bio::TreeIO::svggraph - BioPerl module to export a TreeIO object to svg
• Bio::SeqIO::excel - BioPerl module to read and write sequences into MSExcel-formatted table
• Bio::Tools::Gel - BioPerl module to calculate relative electrophoretic migration distances
• Bio::SeqIO::agave -
• Bio::SeqIO::chadoxml
• Bio::SeqIO::chaosxml
• Bio::SeqIO::strider
• Bio::Tools::Protparam
• Bio::DB::SeqVersion
• Bio::Tools::SiRNA
• Bio::Tools::Analysis::Protein::NetPhos
• Bio::Tools::Analysis::Protein::HNN
• Bio::Tools::Analysis::Protein::GOR4
• Bio::Tools::Analysis::Protein::Domcut
• Bio::Tools::Analysis::Protein::Sopma
• Bio::Tools::Analysis::Protein::Scansite
• Bio::Tools::Analysis::Protein::ELM
• Bio::Tools::Analysis::DNA::ESEfinder
• Bio::Taxonomy
• Bio::DB::CUTG
• Bio::Tools::Run::RemoteBlast - BioPerl interface to a remote BLAST server
• Bio::Tools::Phylo::Gumby -
• Bio::Microarray - Initial repository for microarray-based tools (may be renamed)
• Bio::PhyloNetwork - BioPerl distribution to compute phylogenetic networks
• Bio::Tree::Draw::Cladogram - Bioperl module to draw phylogenetic trees in EPS format
• Bio::Draw::Pictogram - Bioperl module to generate SVG for consensus motif
• Bio::DB::TFBS - BioPerl interface to a Transcription Factor Binding Site database
• Bio::SearchIO::hmmer - BioPerl parser to HMMER output
• Bio::Align::Graphics - BioPerl module to create visual image of sequence alignments
• Bio::AlignIO::stockholm -
• Bio::PopGen - A BioPerl distribution for populations.
• Bio::Phenotype
• Bio::LiveSeq
• emacs::bioperl::mode - Emacs minor mode for BioPerl documentation and template insertion
• Bio::DB::Universal -
• dist::zilla::pluginbundle::bioperl - Dist-Zilla plugin bundle for Bioperl distributions
• Bio::DB::MeSH
• Bio::NeXMLIO - BioPerl distribution for handling NeXML files
• Bio::MolEvol -
• Bio::SeqEvolution -
• Bio::Structure - BioPerl distribution to handle structures
• Bio::Assembly - BioPerl distribution to handle assemblies
• Bio::SearchIO::Writer::BSMLResultWriter - BioPerl BSML BLAST Result Writer
• Bio::Biblio - Bio-Biblio
• Bio::Community - Modules for community biology
• bioperl::pedigree - Linkage analysis research
• bioperl::db - BioPerl BioSQL ORM
• Bio::Tools::Run::Alignment-TCoffee
• Bio::SearchIO::blastxml - BLASTXML modules for BioPerl
• Bio::Coordinate
• bioperl::network - Analysis of protein-protein interactions
• Bundle::BioPerl - Simple Bundle module for BioPerl
• Bio::Staden::iolib - Perl XS bindings to Staden's io_lib
• xml::html -
• task::manager -
• bioperl::papers - BioPerl-specific publication-related data
• bioperl::das::client DAS Client
• Bio::Tools::HMM - BioPerl tools for Hidden Markov Model analysis

For more information, visit bioperl.org.

⇒ BioPerl Modules Installation Options

⇐ BioPerl - Perl Bioinformatics Toolkit

⇑ BioPerl - Perl Bioinformatics Toolkit

⇑⇑ OBF (Open Bioinformatics Foundation) Tools