Bio::Seq - Sequence object, with features River stage two • 60 direct dependents • 65 total dependents

A Seq object is a sequence with sequence features placed on it. The Seq object contains a PrimarySeq object for the actual sequence and also implements its interface. In Bioperl we have 3 main players that people are going to use frequently Bio::Prim...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Root::Test - common base for all BioPerl test scripts River stage two • 60 direct dependents • 65 total dependents

This provides a common base for all BioPerl test scripts. It safely handles the loading of Test::Most, itself a simple wrapper around several highly used test modules: Test::More, Test::Exception, Test::Warn, Test::Deep, and Test::Diff. It also prese...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Tree::Node - A Simple Tree Node River stage two • 60 direct dependents • 65 total dependents

Makes a Tree Node suitable for building a Tree....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SeqIO::bsml - BSML sequence input/output stream River stage two • 60 direct dependents • 65 total dependents

This object can transform Bio::Seq objects to and from BSML (XML) flatfiles....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Root::RootI - base interface for all BioPerl classes River stage two • 60 direct dependents • 65 total dependents

This is just a set of methods which do not assume anything about the object they are on. The methods provide the ability to throw exceptions with nice stack traces. This is what should be inherited by all Bioperl compliant interfaces, even if they ar...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::LocatableSeq - A Bio::PrimarySeq object with start/end points on it that can be projected into a MSA or have coordinates relative to another seq. River stage two • 60 direct dependents • 65 total dependents

The LocatableSeq sequence object was developed mainly because the SimpleAlign object requires this functionality, and in the rewrite of the Sequence object we had to decide what to do with this. It is, to be honest, not well integrated with the rest ...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::erpin - SearchIO-based ERPIN parser River stage two • 60 direct dependents • 65 total dependents

This is an experimental SearchIO-based parser for output from the erpin program. It currently parses erpin output for ERPIN versions 4.2.5 and above; older versions may work but will not be supported....

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Tools::SeqWords - Object holding n-mer statistics for a sequence River stage two • 60 direct dependents • 65 total dependents

Bio::Tools::SeqWords is a featherweight object for the calculation of n-mer word occurrences in a single sequence. It is envisaged that the object will be useful for construction of scripts which use n-mer word tables as the raw material for statisti...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Tools::SeqStats - Object holding statistics for one particular sequence River stage two • 60 direct dependents • 65 total dependents

Bio::Tools::SeqStats is a lightweight object for the calculation of simple statistical and numerical properties of a sequence. By "lightweight" I mean that only "primary" sequences are handled by the object. The calling script needs to create the app...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Location::Simple - Implementation of a Simple Location on a Sequence River stage two • 60 direct dependents • 65 total dependents

This is an implementation of Bio::LocationI to manage exact location information on a Sequence: '22' or '12..15' or '16^17'. You can test the type of the location using length() function () or directly location_type() which can one of two values: 'EX...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Tools::SeqPattern - represent a sequence pattern or motif River stage two • 60 direct dependents • 65 total dependents

Bio::Tools::SeqPattern module encapsulates generic data and methods for manipulating regular expressions describing nucleic or amino acid sequence patterns (a.k.a, "motifs"), such as the ones produced by Bio::Tools::IUPAC. Bio::Tools::SeqPattern is a...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::infernal - SearchIO-based Infernal parser River stage two • 60 direct dependents • 65 total dependents

This is a SearchIO-based parser for Infernal output from the cmsearch program. It currently parses cmsearch output for Infernal versions 0.7-1.1; older versions may work but will not be supported. The latest version of Infernal is 1.1. The output has...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::SearchIO::rnamotif - SearchIO-based RNAMotif parser River stage two • 60 direct dependents • 65 total dependents

This is a highly experimental SearchIO-based parser for output from the rnamotif program (one of the programs in the RNAMotif suite). It currently parses only raw rnamotif output for RNAMotif versions 3.0 and above; older versions may work but will n...

CJFIELDS/BioPerl-1.7.8 - 03 Feb 2021 05:15:14 UTC

Bio::Tree::TreeFunctionsI - Decorated Interface implementing basic Tree exploration methods River stage two • 60 direct dependents • 65 total dependents

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
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