Software from our lab

These are programs that are written to accompany specific papers. In addition, see the programs (or packages)

PHYLIP (Phylogeny Inference Package) which is distributed here.
LAMARC, Mary Kuhner and Jon Yamato's program for Likelihood Analysis using Monte carlo sampling with Random Coalescents. Distributed here.
PopG, a Java program to simulate evolution at one locus with two alleles. Written by Ben Zawadzki and Jim McGill, and descended from earlier versions in other languages starting in the 1970s. For use in teaching population genetics. Distributed here.
Threshml, a program to carry out the MCMC method for both continuous and discrete characters comparative method, described in my 2012 paper in American Naturalist. Can be found here and downloaded from there.

Two locus iteration of gene frequencies, linkage disequilibrium with two linked interacting loci

C program that reads from a file a 3x3 blank-separated matrix of fitnesses for two alleles at two loci, plus recombination fraction and starting gene frequencies and linkage disequilibrium, and allows you to iterate generations and see whether mean fitnesses are increasing or decreasing in each generation

click here to go to folder of program

FORTRAN II program for agglomerative clustering (1964 or 1965, University of Chicago)

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FORTRAN II program for 8-state Camin-Sokal parsimony (1966, University of Chicago)

click here to go to folder of program

FORTRAN IV programs for simulation of the evolution of recombination (Felsenstein, 1974; Felsenstein and Yokoyama, 1976)

click here to go to folder of programs

A warning about compiling the FORTRAN IV programs: They use the operator .AND. to do bitwise AND operations. This may work in FORTRAN 77, as there is backwards compatibility in it. In Gnu FORTRAN it will work if you use the -fdec flag with the compiler. Otherwise it may be necessary to change expressions like M.AND.N to IAND(M, N) or to AND(M,N).

Speciation model programs

Pascal programs for the 1981 paper in Evolution: "Skepticism towards Santa Rosalia, or Why are there so few kinds of animals?"

click here to go to folder of programs