get the ultrametric trees

[nilofar alaie]

Hi all, 

I have gene tress that I got from the iqtree, now i want to use the PAML to convert them to ultrametric trees, (set the global molecular clock and use a single evolutionary rate). 

Do you know how i can do this process in PAML? 

Thanks and with the best

Niloo

[Sishuo Wang]

Hi Niloo,

If only a rough estimate and a rapid conversion, there should be many tools but one option is chronos from the "ape" (https://cran.r-project.org/web/packages/ape/ape.pdf). More details about the method can be found in the reference below. Otherwise, maybe MCMCTree manual.

library('ape')

tree <- read.tree(tree_file)

dendrogram <- chronos(tree)

write.tree(dendrogram)

References

1. Sanderson, M. J. (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101–109

Sishuo

[Ziheng]

yes, you can use mid-point rooting to root the tree.

you can use baseml with clock = 1 to estimate the branch lengths under the strict clock.

either way, what you are doing is sensible only if the clock is not seriously violated, because clock rooting is unreliable if the clock is seriously wrong.

best, ziheng