Question: Is there any tool available to generate ultrametric tree from a rooted phylogenetic tree?
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gravatar for Dineshkumar K
10 months ago by
Kasaragod, Kerala, India
Dineshkumar K40 wrote:

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.

R unix python perl phylogeny • 603 views
ADD COMMENTlink modified 10 months ago by Brice Sarver3.5k • written 10 months ago by Dineshkumar K40

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.

ADD REPLYlink written 9 months ago by _r_am31k
0
gravatar for Brice Sarver
10 months ago by
Brice Sarver3.5k
United States
Brice Sarver3.5k wrote:

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.

ADD COMMENTlink written 10 months ago by Brice Sarver3.5k
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