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The citation for this code should be the paper that I originally developed it for:

@article{Thornton:2005il, author = {Thornton, Kevin and Long, Manyuan}, title = {{Excess of amino acid substitutions relative to polymorphism between X-linked duplications in Drosophila melanogaster.}}, journal = {Molecular Biology and Evolution}, year = {2005}, volume = {22}, number = {2}, pages = {273--284}, month = feb }

Alternately, I'm fine if you cite the libsequence original paper:

@article{Thornton:2003vz, author = {Thornton, Kevin}, title = {{Libsequence: a C++ class library for evolutionary genetic analysis.}}, journal = {Bioinformatics (Oxford, England)}, year = {2003}, volume = {19}, number = {17}, pages = {2325--2327}, month = nov }