Thanks, guys. I just have a follow-up question: Does anyone know of a
way to optimize BLs using optim.pml() while enforcing a molecular
clock?
Thanks!
John
On Thu, Nov 8, 2012 at 6:06 PM, Rob Lanfear rob.lanf...@gmail.com wrote:
Hi John,
Brian's suggestion is a good one.
Another option
Hi John,
optim.pml has an parameter optRooted and you have to set it to TRUE.
If you give the function an ultrametric tree it will optimise the edge
lengths. Unfortunately it is not possible to use tree rearrangements
with this option so far.
Regards,
Klaus
On 11/9/12, john d
Hi there,
I have a well-supported phylogeny (with branch lengths proportional to
absolute time) and I'm interested in estimating the mutation rate of
an independently-obtained molecular dataset. Any suggestions?
thanks!
John
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R-sig-phylo mailing
If you want the branch-specific substitution rate, you could estimate the
branch lengths on a topology constrained to match the chronogram, then
divide each of the molecular tree's branch lengths by the corresponding
chronogram branch lengths to get these rates. If you want a global rate,
you
