Foreground branch lengths in branch and branch site models are very different to original branch lengths.

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Mar 22, 2019, 6:22:54 AM3/22/19

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Hi,

I am getting branch lengths using M0 model for my treefile and using them as initial values for branch and branch site models.

When I mark a branch of interest as foreground in the above models,that branch sometimes has a length significantly different than M0 length.

for eg. sometimes its scaled by a huge amount. - M0 branch length 1.8 becomes 50.5 or something with branch model,15.5 with branch site model A etc.

I am not sure why such a difference - is it because different models have different parameters? Is it okay to trust the results?

Running it multiple times with different starting omega to check for convergence gives me the same set of results- branch length,omega values etc.

Regards,

Vigzy

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Mar 30, 2019, 5:29:24 AM3/30/19

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perhaps the foreground branch has a large w, which then makes the branch length very large, but the difference you mentioned does sound very large.

if you send me a copy of the files to duplicate the problem, i can try to take a look.