UNDER CONSTRUCTION...
**McDonald-Kreitman Test (McDonald & Kreitman 1991)**
Please cite the following when using this script:
Holloway, A.K., M.K.N. Lawniczak, J.G. Mezey, D.J. Begun, and C.D. Jones. 2007. Adaptive gene expression divergence inferred from population genomics. PLoS Genetics 3:2007-2013.
type 'MK.pl' to get usage info
-returns MK test counts and FET pvalue
-can be polarized or unpolarized - max 2 outgroups for polarized
-takes path that minimizes nonsynonymous changes between AAs
-does not use sites that include codons with ambiguity (Ns)
-ingroup can only have 3 unique codons at a site, otherwise skipped
-for polarized tests, both outgroups must have same codon, otherwise skipped
FASTA FILE FORMAT
-expects fasta format files with species name first, followed by
a semicolon and then can have other information or not.
-file names should be *.fa
NOTE: you will need to have the module Text::NSP to get the FET
please send any questions|error reports to akholloway at ucdavis dot edu