Search results for "distribution:BioPerl ALLENDAY"
Bio::TreeIO - Parser for Tree files
This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::kegg - KEGG sequence input/output stream
This class transforms KEGG gene records into Bio::Seq objects. Mapping of record properties to object properties This section is supposed to document which sections and properties of a KEGG databank record end up where in the Bioperl object model. It...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SimpleAlign - Multiple alignments held as a set of sequences
SimpleAlign is an object that handles a multiple sequence alignment (MSA). It is very permissive of types (it does not insist on sequences being all same length, for example). Think of it as a set of sequences with a whole series of built-in manipula...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AnnotatableI - the base interface an annotatable object must implement
This is the base interface that all annotatable objects must implement. A good example is Bio::Seq which is an AnnotableI object....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::AlignIO::maf - Multiple Alignment Format sequence input stream
This class constructs Bio::SimpleAlign objects from an MAF-format multiple alignment file. Writing in MAF format is currently unimplemented. Spec of MAF format is here: http://genome.ucsc.edu/FAQ/FAQformat...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::OntologyStore - A repository of ontologies
The primary purpose of this module is that of a singleton repository of Bio::Ontology::OntologyI instances from which an Ontology instance can be retrieved by name or identifier. This enables TermI implementations to return their corresponding Ontolo...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Ontology::DocumentRegistry - Keep track of where to find ontologies. Allows lookups by name.
Do not use this directly, use Bio::Ontology::OntologyStore instead. Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to load and cache ontologies as object graphs, you can just ask it for what you want by name. See Bio::Ontology::Ont...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::OntologyIO::simplehierarchy - a base class parser for simple hierarchy-by-indentation type formats
Needs Graph.pm from CPAN. This class is nearly identical to OntologyIO::dagflat, see Bio::OntologyIO::dagflat for details....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC