<p>I'm using PhyML to compute phylogenetic trees. In principle, there's a parallel option (via MPI), but it doesn't work for me. Instead of spending lots of time debugging MPI, I was wondering if I could run the bootstraps independently (with a user-supplied tree) on my cluster. So the real question is: Given a list of trees in Newick format, how do I calculate the bootstrap support for the original tree?</p>

<p>You can use an strategy similar to what Phylip does. You can generate 1000 random input files with SEQBOOT and use these files in PhyML, not in a real parallel mode, but in parallel as starting different PhyML processes in different nodes/cores at the same time (using something like <a href="http://code.google.com/p/ppss/">this</a>. </p>
<p>At the end CONSENSE will calculate a consensus tree and give you the actual bootstrap values.</p>