ah, okay, thanks for the links.The current standard is being compiled by the HapMap project:
http://hapmap.ncbi.nlm.nih.gov/
You can input a gene and look at the alleles they have found for that gene, the percentage of their test populations that have that allele, and so forth. I don't know if this will work, but here is a copied url for a search I did for the human mmp13 gene. Included on the page are the SNPs (single nucleotide polymorphisms) and the frequency of those SNPs in the populations they looked at.
http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap28_B36/#search
This seems to be a simple list of some of the more important equations used in population genetics:
http://www.radford.edu/~rsheehy/Gen_flash/ABLE_Workshop/Popgen_Equations.pdf
Here is another reference:
http://www.nyu.edu/projects/fitch/courses/evolution/html/genetic_drift.html
If you have estimates for the mutation rate and effective population sizes you can make predict how much divergence there should be between two species over a certain amount of time.
but there seems to be a problem.
these do not model a bacteria becoming a human, or a tree, or a cat.
i'm quite confident that you can model populations, such as a group of humanoids, or a group of canines.
but these aren't phylogenic changes.
i don't think the above equations model the major transitions maynard smith speaks about.
this is what i really want.
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