Bio::fastAPD

The Bio::fastAPD module provides computationally efficient methods for the
calculation of average pairwise difference (APD), a measure of nucleotide 
diversity, from multiple sequence alignment (MSA) data. The module also 
provides rapid standard error estimation of the APD using an efficient 
jackknife resampling method. Further description of the methods implemented
in this module, including mathematical justification, will be available in 
an upcoming peer-reviewed journal article.  


INSTALLATION

To install this module, run the following commands from within the fastAPD
directory:

	perl Makefile.PL
	make
	make test
	make install

To install this module into a specific directory:
   	perl Makefile.PL PREFIX=/name/of/the/directory


EXAMPLE

An example script is provided along with example data consisting of 1000 
aligned dna reads. 

       perl example_script.t


LICENSE AND COPYRIGHT

Copyright (C) 2014,2015 Joseph D. Baugher


This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published
by the Free Software Foundation; or the Artistic License.

See http://dev.perl.org/licenses/ for more information.