Author image Arlin Stoltzfus

Documentation

Bio::NEXUS Installation Instructions.
Hands-on tutorial for using Bio::NEXUS module.
translate an alignment into NEXUS format using BioPerl
do something very important.
create a new NEXUS from OTU set of another NEXUS file
do something very important.
Trees as strings
PostScript plot of tree + data table (from NEXUS infile)
Command-line NEXUS file manipulation tool
uses R to create PPP trees from a NEXUS file
generates posterior probability of presence plots (SPAN)
translate a tree in DND or phylip format into NEXUS TREES block

Modules

An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format
Represents ASSUMPTIONS block of a NEXUS file
Provides useful functions for blocks in NEXUS file (parent class).
Represents a CHARACTERS Block (Data or Characters) of a NEXUS file
Represents CODONS block in NEXUS file
Represents the deprecated DATA Block in NEXUS file.
Represents DISTANCES block in NEXUS file
Provides private utiliy functions for the module
Represents a HISTORY block of a NEXUS file
Provides functions for handling blocks that have matrices
Provides functions for manipulating nodes in trees
Provides functions for manipulating nodes in trees
Represents a NOTES block in a NEXUS file.
Represents SETS block of a NEXUS file
Represent SPAN block in a NEXUS file (contains meta data).
Represents a taxon unit in a NEXUS file
Represents a sets of OTUS (Bio::NEXUS::TaxUnits objects) in a NEXUS file
Represents TAXA block of a NEXUS file
represents a character block (Data or Characters) of a NEXUS file
NEXUS file content modifier ( exclude/select/rename options on OTUs).
PostScript plot of tree + data table (from NEXUS infile)
Provides functions for manipulating trees
Represents TREES block of a NEXUS file
Represents an UNALIGNED block of a NEXUS file
Represents a simple object for storing information unrecognized blocks by the Bio::NEXUS module.
Exception classes for Bio::NEXUS.
Logging for Bio::NEXUS.
Represents column weights in alignment ( for each character)

Provides

in lib/Bio/NEXUS/Util/Exceptions.pm

Examples