README file for the NEXPL library with accompanying tools.
$Id: README,v 1.10 2006/08/24 19:40:06 arlin Exp $

ABOUT

The NEXPL package contains the Bio::NEXUS library, providing 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. 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).

LICENSE & ACKNOWLEDGEMENTS

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. 

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. 




