I am working trying to decipher two large phylogenies and I am wondering about how to estimate confidence. In the past I had estimated confidence using boostrap and posterior probability when doing bayesian phylogenetic inference. Now I am following up on the work but the databases have grown immensely to 15000-30000 sequences. What is the approach for having some kind of confidence on the phylogeny?:
- Bootstrap or posterior probabilities on big phylogenes, is it possible or sensible?? My concern is that it seems that with bootstraps it just takes a single - very divergent - sequence "jumping around" to invalidate the bootstraps.
- reducing the phylogeny to a small enough set of sequences that would make it manageable? If we are mostly interested in the deeper branches does this make sense?
Thanks in advance, any help appreciated