README file for the NEXPL library with accompanying tools. $Id: README,v 1.13 2007/04/02 20:22:30 mike Exp $ ABOUT The Bio::NEXUS package provides an object-oriented, Perl-based applications programming interface (API) to the NEXUS file format of Maddison, et al., 1997 (Syst. Biol. 46:590-621). 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. NEXUS 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). LICENSE & ACKNOWLEDGEMENTS The Bio::NEXUS 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 from http://www.cpan.org. INSTALLATION AND TESTING Note that before installing Bio::NEXUS, you need the following modules installed on your system: Clone::PP (1.02 or higher) Test::More Test::Deep (if you are using the CPAN tool, it should install those dependencies automatically, though it hasn't been tested) This software has been tested under Linux as well as Mac OS 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. DOCUMENTATION All of the modules are documented internally with POD, and the doc directory has Tutorial, Installation, User Manual documents. You can read these online at CPAN, or access your local copies with a command like these: perldoc NEXUS.pm # give path to file perldoc Bio::NEXUS # installed module perldoc nexplot.pl # installed executable in your exec path perldoc doc/UserManual.pod FEEDBACK We welcome feedback from end-users and developers. Please write to Arlin Stoltzfus by email at .nist.gov.