bPTP server: a Bayesian implementation of the PTP model for species delimitation

with PhyloMap for visualization
Please cite: A General Species Delimitation Method with Applications to Phylogenetic Placements. Zhang, Jiajie, Kapli, P., Pavlidis, P., and Stamatakis, A. Bioinformatics (Oxford, England)(2013), 29 (22): 2869-2876

bPTP is an updated version of the original maximum likelihood PTP (maximum likelihood PTP search result is part of the bPTP results), it adds Bayesian support (BS) values to delimited species on the input tree. Higher BS value on a node indicates all descendants from this node are more likely to be from one species. Note this web server only allows a single phylogenetic tree as input - to run on multiple trees (from Bayesian analysis or bootstrap), please download the bPTP and PTP standalone.
If you are not familiar with Bayesian analysis, please read this first.
The server will only accept Newick format or NEXUS format with no annotations on the tree.
Here is an example of Newick format and an example of NEXUS format.
Special note on taxa name: A valid taxa name should only contains letters, numbers, _ and -; and should NOT be pure numbers. Any other characters, in particular space, $, #, %, ( and ), will cause errors!

If unrooted, the tree will be rooted at the longest branch.

For small trees (<50 taxa), 100000 is usually enough, but you should always check for convergence.

Always check if more burn-in is needed.

Change the seed if MCMC chains does not converge.

e.g. t1 t2 t3, taxa name separated by a single space, if specified, the tree will be rerooted accordingly.

Remove outgroups that are distant related can improve the delimitation results.

You can use it to find your results later.