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Code is available to calculate divergence and convergence using modifications (corruptions? mutations?) of the codeml program from Ziheng Yang's PAML4 package. This software calculates posterior convergent and divergent substitution probabilities and their expected counts using posterior integration and amino acid substitution models: "codeml-ancestral". Please see readme file for more information. Code credits to Jason de Koning. |
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Code package (.gz): ReadMe codeml.c codeml.ctl Makefile Nuc.tree paml.h pamp.c squamateMtCDS.phy tools.c treespace.c treesub.c dat/jones.dat dat/mtmam.dat dat/mtREV24.dat |
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Evidence for an ancient adaptive episode of convergent molecular evolution,
Todd A. Castoe,
A. P. Jason de Koning,
Hyun-Min Kim,
Wanjun Gua,
Brice P. Noonan,
Gavin Naylor,
Zhi J. Jiang,
Christopher L. Parkinson and
David D. Pollock, PNAS, 2009
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