Arlin Stoltzfus > Bio-NEXUS-0.78

Bio-NEXUS-0.78

This Release Bio-NEXUS-0.78  [Download] [Browse 10 Feb 2012
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Special Files
Build.PL
doc/changes
LICENSE
Makefile.PL
MANIFEST
META.yml
README

Modules

Bio::NEXUS An object-oriented Perl Applications Programming Interface (API) for the NEXUS file format     0.78
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::Matrix Provides functions for handling blocks that have matrices      
Bio::NEXUS::NHXCmd Provides functions for manipulating nodes in trees      
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::Tools::GraphicsParams      
Bio::NEXUS::Tools::NexModifier      
Bio::NEXUS::Tools::NexPlotter      
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::Util::Exceptions Exception classes for Bio::NEXUS.      
Bio::NEXUS::Util::Logger Logging for Bio::NEXUS.      
Bio::NEXUS::WeightSet Represents column weights in alignment ( for each character)      

Documentation

Bio::NEXUS::Tools::Modifier NEXUS file content modifier ( exclude/select/rename options on OTUs).  
Bugs Report for the NEXPL library  
Graphics represents a character block (Data or Characters) of a NEXUS file  
Installation Bio::NEXUS Installation Instructions.  
Tutorial Hands-on tutorial for using Bio::NEXUS module.  
align2nex.pl translate an alignment into NEXUS format using BioPerl  
extract_taxset.pl create a new NEXUS from OTU set of another NEXUS file  
history.pl  
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  
p3treeplot.pl uses R to create PPP trees from a NEXUS file  
pppplot.pl generates posterior probability of presence plots (SPAN)  
this.pl do something very important.  
tree2nex.pl translate a tree in DND or phylip format into NEXUS TREES block  

Other Files

README_admin
doc/NEXUS_coverage.html