Bio::NEXUS::SetsBlock is a Perl module that represents SETS block of a NEXUS file.

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file.

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file.

Bio::NEXUS::UnalignedBlock is a Perl module that represents an UNALIGNED block of a NEXUS file.

Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character).

Bio::Ontology::GOterm is a representation of GO terms.

Bio::Ontology::Ontology is a standard implementation of an Ontology.

Bio::OntologyIO::simplehierarchy is a base class parser for simple hierarchy-by-indentation type formats.

Bio::Phylo::Manual is a Perl module that contains a Bio::Phylo v.0.14 user guide.

Bio::Phylo::Treedrawer::Svg is a Perl module that creates svg tree drawings.

Bio::PrimarySeqI is a Perl Interface definition for a Bio::PrimarySeq.

Bio::Restriction::Enzyme is a single restriction endonuclease (cuts DNA at specific locations).

Bio::Root::Object is a core Perl 5 object.

Bio::Seq is a sequence object, with features.

Bio::SeqIO::fastq is a fastq sequence input/output stream.

Bio::Tools::AlignFactory is a base object for alignment factories.

Bio::Tools::Run::JavaRunner is a Perl module that can run java programs.

Bio::Tools::Run::PiseApplication::align2model is a Bioperl class for align2model - create a multiple alignment of sequences...

Bio::Tools::Run::PiseApplication::charge is a Perl module.

Bio::Tools::Run::PiseApplication::consensus is a Perl module.

Bio::Tools::Run::PiseApplication::fasta is a Bioperl class for sequence database search.

Bio::Tools::Run::PiseApplication::freak is a Perl module.

Bio::Tools::Run::PiseWorkflow is a class to create a Pise workflow using Pise application objects as methods.

Bio::Tools::Run::TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'.

Bio::Tree::NodeNHX is a Simple Tree Node with support for NHX tags.