Is there any tool available to generate ultrametric tree from a rooted phylogenetic tree?

Question

[Kumar]

I need to generate ultrametric tree from a rooted phylogenetic tree. Therefore, please suggest me any tool which can do the same. Many thanks in advance.

[Ram]

Hello Dineshkumar K!

It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/11437/how-to-generate-ultrametric-phylogenetic-trees

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[Brice Sarver]

If you're unwilling to or can't calibrate your phylogeny by placing prior distributions on node ages in BEAST (for example), you can try using a few other approaches. Nonparametric rate smoothing is implemented in the R package ape. This is also implemented in r8s, along with PL and ML methods. I've had good results using treePL for some of my previous work.

Be aware that making a tree ultrametric is more than simply 'making the tips equal,' hence my model-based suggestions above.