I'm using BEAST v1.10.4 and I can generate a phylogenetic tree which displays nicely in figtree v1.4.4. When I select node labels on the left side of the figtree interface it has options to display things such as height, length, posterior, rate, ect. However, I do not see any option that says bootstrap to display bootstrap values. Is there something I need to do in the BEAST program or TreeAnnotator to output the bootstrap values so that Figtree can display? or this not possible with BEAST?
Hi David,
Beast makes a Bayesian inference of phylogeny. There are no bootstrap values to show, because they are not calculated. The measure of confidence or support is the posterior probability of the MCMC chain.
You can find more information here:
https://beast.community/
Cheers,
Camilo
Dear David
The phylogenetic tree by Beast is not a maximum likelihood tree and does not include bootstrap replicates. It is a Bayesian tree. So you can use Bayesian posterior probabilities to assess branch support of the BI tree.
Good luck
Afsaneh