Extract age estimates from a very large phylogeny.

[Alex H]

Hi all, 

I am trying to find a more functional way to extract age estimates(node heights) from a dated consensus phylogeny. Currently I am only able to extract the age estimates which I am interested in by opening my annotated NEXUS file in FigTree and displaying "heights_95%_HPD" as node labels, however the size of the tree file (20,000 + taxa) makes FigTree terribly slow and frustrating to work with. So I hope there is an easier way for me to obtain the minimum and maximum 95% height values for a number of "nodes of interest" without using FigTree.

In the past I have used the branching.times() R function to avoid the click and zoom functionality of FigTree, but this function does not return min and max heights and certainly doesn't work with multiphylo objects

Hopefully somebody with more experience with such large datasets can help me figure out an effective work around. 

Regards 

Alex

[langgeng agung]

Hi Alex,

I think for your purpose, it is better to group your taxa into several groups/clades which you want to estimate the age. Then, of your interest groups, you may want to make a MRCA prior on your BEAST analysis. Therefore, it may display the estimated age and the 95%HPD when you open the logfile on the Tracer.

hope this help,

cheers,

Langgeng

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[Jonathan Chang]

Hi Alex,

I had a similar issue a few years ago and wrote a Python script to extract age estimates from beast summary trees. I believe it still works but feel free to contact me if you encounter issues. 

https://github.com/jonchang/beastcommentparser

Sent from my iPhone

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[Alex H]

Thanks for the suggestions, @langgen agung and @Jonathan Chan, I also received a private message to explore the functions of the R package phylotate. which makes it possible to read in a Nexus/Newick file as well as the annotations. It is then possible to print out the comments per node of interest. I am able to solve my problem relatively easy this way.

In any regard your advice is much appreciated 

Alex