Hi-
I'd like to calculate a Tmrca for a sample of DNA sequences that has
evidence of recombination (including at least one gene conversion) and
possibly is under selection...I have been finding that people use somthing
like FLUCTUATE, COALESCE, or GENETREE, which basically assume no
recombination. (Often these data sets, do, in fact have evidence of
recombination or selection.) Another method seems to be timing the
sequences in a slightly more basic way: just averaging diffs and using
average diffs with an outgroup and a calibration date to obtain Tmrca.
What are my options? What is thebest option? I'd 'like' to have a date.
Will recombination systematically bias the Tmrca up or down in these
programs? Is the simple method a good way forward, given all the caveats
for using the other programs? (Is there a good reference for the simple
averaging method?)
Thanks (again) for the help,
Michael
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