by R. C. Griffiths
A unique gene tree describing the mutation history of a sample of DNA sequences can be can be constructed as a perfect phylogeny under an assumption of non-recurrent point mutations. Genetree constructs such trees from DNA data and computes maximum likelihood estimates of mutation, migration and growth rates in the population. It also computes the distribution of the time to the most recent common ancestor and ages of mutations in gene trees. Geographical information as to which subpopulation mutations occurred in and where the most recent common ancestor of the sequences was is also computed. A companion program treepic has flexible output for producing postscript gene tree pictures. Version 9.0 is much faster in generating times in subdivided and exponentially growing populations than Version 8.3.
Source code is available and a compiled version for PC use are included in the zip file. The source code is portable and compiles under gcc.
[Zip file of source code]