Search results for "distribution:BioPerl AMACKEY"
Bio::Seq::Meta - Generic superclass for sequence objects with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See Bio::LocatableSeq and Bio::Seq::MetaI. Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::SeqIO::pir - PIR sequence input/output stream
This object can transform Bio::Seq objects to and from pir flat file databases. Note: This does not completely preserve the PIR format - quality information about sequence is currently discarded since bioperl does not have a mechanism for handling th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Tree - An implementation of the TreeI interface.
This object holds handles to Nodes which make up a tree....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::Node - A Simple Tree Node
Makes a Tree Node suitable for building a Tree....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::MetaI - Interface for sequence objects with residue-based meta information
This class defines an abstract interface for basic residue-based meta information. Examples of this kind of meta data are secondary structures (RNA and protein), protein hydrophobicity assignments, or other alternative alphabets for polypeptides, seq...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::TreeIO::nhx - TreeIO implementation for parsing Newick/New Hampshire eXtendend (NHX) format.
This module handles parsing and writing of Newick/New Hampshire eXtended (NHX) format....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::TreeI - A Tree object suitable for lots of things, designed originally for Phylogenetic Trees.
This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::NodeI - Interface describing a Tree Node
A NodeI is capable of the basic structure of building a tree and storing the branch length between nodes. The branch length is the length of the branch between the node and its ancestor, thus a root node in a Tree will not typically have a valid bran...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tools::IUPAC - Generates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
Bio::Tools::IUPAC is a tool that manipulates sequences with ambiguous residues following the IUPAC conventions. Non-standard characters have the meaning described below: IUPAC-IUB SYMBOLS FOR NUCLEOTIDE (DNA OR RNA) NOMENCLATURE: Cornish-Bowden (1985...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::NodeNHX - A Simple Tree Node with support for NHX tags
Makes a Tree Node with NHX tags, suitable for building a Tree. See Bio::Tree::Node for a full list of functionality....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::EncodedSeq - subtype of Bio::LocatableSeq to store DNA that encodes a protein
Bio::Seq::EncodedSeq is a Bio::LocatableSeq object that holds a DNA sequence as well as information about the coding potential of that DNA sequence. It is meant to be useful in an alignment context, where the DNA may contain frameshifts, gaps and/or ...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Seq::Meta::Array - array-based generic implementation of a sequence class with residue-based meta information
This class implements generic methods for sequences with residue-based meta information. Meta sequences with meta data are Bio::LocatableSeq objects with additional methods to store that meta information. See Bio::LocatableSeq and Bio::Seq::MetaI. Th...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Processor - DESCRIPTION of Object
Describe the object here...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::HitI - Interface for a hit in a similarity search result
Bio::Search::Hit::* objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Hit::Fasta - Hit object specific for Fasta-generated hits
Bio::Search::Hit::HitI objects are data structures that contain information about specific hits obtained during a library search. Some information will be algorithm-specific, but others will be generally defined, such as the ability to obtain alignme...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods
This interface provides a set of implemented Tree functions which only use the defined methods in the TreeI or NodeI interface....
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC
Bio::Search::Result::ResultI - Abstract interface to Search Result objects
Bio::Search::Result::ResultI objects are data structures containing the results from the execution of a search algorithm. As such, it may contain various algorithm specific information as well as details of the execution, but will contain a few funda...
CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC