Hello,
I would like to date certain nodes within a molecular phylogeny by
calibrating other parts with fossil dates and using the branch lengths
of a clock-constrained tree as units of time. Unfortunately, a recent
test I did found the clock constrained tree was significantly less
likely than the unconstrained tree, but was also a different topology.
These are ML trees based on a GTR+I+G model. Could anyone out there
offer a succinct explanation for what a program such as PAUP is doing as
it forces a molecular clock constraint? Why would the topology have to
change? Is there any reason to pinpoint sequences that look like they
have long branches in the unconstrained tree to leave out? What about
those sequences that jump around between constrained and unconstrained
trees? Is it "fair" or statistically valid to sequentially remove
outliers until the tree behaves in a clock-like manner? I have seen
this latter technique used, but was curious about what the general
opinion is.
Thanks,
Chris
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