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Bio-NEXUS-0.67
River stage one • 1 direct dependent • 1 total dependent
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Documentation

Installation
Bio::NEXUS Installation Instructions.
Tutorial
Hands-on tutorial for using Bio::NEXUS module.
align2nex.pl
translate an alignment into NEXUS format using BioPerl
nex2text_tree.pl
Trees as strings
nexplot.pl
PostScript plot of tree + data table (from NEXUS infile)
nextool.pl
Command-line NEXUS file manipulation tool

Modules

Bio::NEXUS
An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
Bio::NEXUS::AssumptionsBlock
Represents ASSUMPTIONS block of a NEXUS file
Bio::NEXUS::Block
Provides useful functions for blocks in NEXUS file (parent class).
Bio::NEXUS::CharactersBlock
Represents a CHARACTERS Block (Data or Characters) of a NEXUS file
Bio::NEXUS::CodonsBlock
Represents CODONS block in NEXUS file
Bio::NEXUS::DataBlock
Represents the deprecated DATA Block in NEXUS file.
Bio::NEXUS::DistancesBlock
Represents DISTANCES block in NEXUS file
Bio::NEXUS::Functions
Provides private utiliy functions for the module
Bio::NEXUS::HistoryBlock
Represents a HISTORY block of a NEXUS file
Bio::NEXUS::MatrixBlock
Provides functions for handling blocks that have matrices
Bio::NEXUS::Node
Provides functions for manipulating nodes in trees
Bio::NEXUS::NotesBlock
Represents a NOTES block in a NEXUS file.
Bio::NEXUS::SetsBlock
Represents SETS block of a NEXUS file
Bio::NEXUS::SpanBlock
Represent SPAN block in a NEXUS file (contains meta data).
Bio::NEXUS::TaxUnit
Represents a taxon unit in a NEXUS file
Bio::NEXUS::TaxUnitSet
Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file
Bio::NEXUS::TaxaBlock
Represents TAXA block of a NEXUS file
Bio::NEXUS::Tree
Provides functions for manipulating trees
Bio::NEXUS::TreesBlock
Represents TREES block of a NEXUS file
Bio::NEXUS::UnalignedBlock
Represents an UNALIGNED block of a NEXUS file
Bio::NEXUS::UnknownBlock
Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module.
Bio::NEXUS::WeightSet
Represents column weights in alignment ( for each character)

Other files