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 <myfirstname>.<mylastname><at>nist.gov. 




