While there are various programs that will use values for transitions vs
transversions, we haven't been able to find a program that produces these
values. MacClade does something of the sort, but the values are based on
a tree, and we would like to use them to create the tree. Programs in
Pyhlip also allow one to set these values, but again it's not clear that
there is anything in the package that calculates the values. Can anyone
steer us in the right direction?
tom_doak at hlthsci.med.utah.edu