Patterns of DNA polymorphisms observed within populations can be used to understand the processes of demography, adaptation, and ultimately speciation. These patterns are typically quantified using the site frequency spectrum. The shape of this spectrum is understood theoretically under genetic drift, various demographic scenarios and with some forms of natural selection. DNA Sequence Analysis and Manipulation (DnaSAM), addresses the challenges of data manipulation, summary statistic estimation and statistical hypothesis testing for large-scale resequencing projects. The program is capable of performing a large number of standard and newly designed tests of neutrality for multiple sequence alignments of resequenced gene loci. In addition, the program allows hypothesis testing using complex and user-specified null models.
DnaSAM is written for Perl (version 5) and has been tested in both Apple's OS 10.5 and Fedora Core Linux 8 environments and should be compatible with any environment where Perl 5 is installed.
DnaSAM uses output from Richard Hudson's ms program, and he has made
the source code and documentation for ms available at the following
site:
http://home.uchicago.edu/~rhudson1/source/mksamples.html
If you already have ms installed on your computer, you can download
the dnasam.<version>_source.tar.gz file and follow the instructions in
the dnasam.pdf manual to install DnaSAM and create a symbolic link to
the ms binary.
As a convenience, we've created compiled ms binaries for both
GNU/linux and Apple's OS 10.5 that we've included in the
dnasam.<version>linux_x86.tar.gz and dnasam.<version>_osx_x86.tar.gz
files. If you are running one of these operating systems and do not
wish to compile and install ms, you can download one of these files.
