How to generate ultrametric phylogenetic trees?

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I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss.

I have generated rooted species tree with 1000 bootstraps by RAxML. Further, I need to generate ultrametric tree for the same. Therefore, Please suggest me how to generate ultrametric tree from the rooted species tree.

Thank you.

Answer 1

An ultrametric tree is simply a global molecular clock and can be easily generate in PAML using a single evolutionary rate. You take you RAxML tree in phylip format (PAML might do nexus format know), and click the "clock function". PAML will do the rest.

You can alternatively generate it de novo via UPGMA neighbor-joining tree which is found in the MEGAX package (which is probably easier and considered a technical definition of an ultrametric tree).

A global molecular clock (as opposed to a local molecular clock) is quite a specific request, but if you performed a likelihood ratio test, it would identify "clock-like" behaviour.