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.