Bio::NEXUS

Description

Bio::NEXUS is a Perl module providing an object-oriented, Perl-based applications programming interface (API). NEXUS is a powerful and extensible format designed for use in evolutionary analysis, including the analysis of molecular sequence data as well as classical morphological and life-history data. It is the input or output format for software such as PAUP*, MacClade, Mesquite, SIMMAP, MrBayes, Nexplorer, and so on. This package also contains the demonstration applications nexplot.pl (plot character data with a tree) and nextool.pl (allowing programmatic editing, e.g., selecting particular clades or subsets of data). The NEXPL library of Perl software (copyright 2004 Liang, Qiu and Yang) is distributed under an open source license (see LICENSE). If you use this software, please acknowledge: Bio::NEXUS. An Object-oriented NEXUS API in Perl. T.J. Hladish, C.L. Liang, W.-G. Qiu, P. Yang, V. Gopalan and A. Stoltzfus. Available at http://www.molevol.org/camel/software. INSTALLATION AND TESTING This software has been tested under Linux as well as MaxOS X 10.2 and higher, and even a few Windows installations. The package installs using the standard procedure, and runs several hundred tests: perl Makefile.PL make make test make install For more information, or to customize, see doc/Installation.pod..

Nexus - Api - Bionexus - Applications Programming Interface - Programming Interface - Perl Module - Applications Programming - Perl - Applications - Object-Oriented - Providing - Software - Programming - Libraries

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Bio::NEXUS::WeightSet is a Perl module that represents column weights in alignment ( for each character).

Bio::NEXUS::HistoryBlock is a Perl module that represents a HISTORY block of a NEXUS file.

Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees.

Bio::NEXUS::TaxaBlock is a Perl module that represents TAXA block of a NEXUS file.

Bio::NEXUS::TreesBlock is a Perl module that represents TREES block of a NEXUS file.