Hello Ashwini,

You can find the std using the software TRACER. Follow this link http://beast.bio.ed.ac.uk/analysing-beast-output

Best wishes,

Ana

Hi Ana

I saw this link before also however I am unable to find std dev for nodes of my ingroup. Out group information i could extract as those nodes are defined by me . But how to i find it for various nodes in my ingroup.

Hi Ashwini,

I really don`t know how to get the std dev for each node, but as you noted already you can get the 95%hdp from figtree

Hi Ashwini,

Typically, you would first need to define your ingroup in BEAUti's Taxon Sets tab. After running your analyses, as Ana mentions, you would upload your logfile (.log) in Tracer to look at different statistics of the time-to-the-most-recent-common-ancestor (TMRCA) of your ingroup.

In the event that you did not specify a taxon group in BEAUti, and you are unwilling to repeat your analysis, another option is to use R:

For instance, you could use the ape package (read.nexus function) to upload the whole posterior distribution of trees (your .trees file). After discarding the burnin, you could loop-search and extract the node age of your ingroup. Once you have the node ages in a vector, you can do whatever kind of statistics on it (e.g. using mean() and std() functions). This approach requires a bit of knowledge on how to deal with tree data in R, and R in general. Have a look at the attached link if you are interested.

Cheers,

Santiago

http://www.phytools.org/eqg/Exercise_3.2/