Efficient Programme To Construct Trees With A Given Fixed Topology

Question

[Biojl]

Hi,

Could you recommend me some efficient command-line software to generate trees (i.e. N-J) from alignments given a fixed topology as input?

Thanks! JL

Answer 1

[Josh Herr]

Most, if not all, phylogenetic analysis programs will let you constrain a topology for hypothesis testing.

I like RAxML for maximum likelihood based methods (github here) and MrBayes (sourceforge here) for Bayesian analysis. Mesquite is helpful for me when considering character-based topology constraints. There are lots of programs out there, but I probably use these three the most. My favorite tree viewer is FigTree.

As usual, you'll have to read the manuals of all of the tools to figure out how to constrain your topology from the command line, but I usually do this from within my nexus file.

[DG]

I second RAxML with topology constraints, if you have a fixed topology. I always recommend doing ML or Bayesian analyses over NJ or distance methods wherever possible and if your topology is constrained the lengthiest part of tree reconstruction is handled. So it should be quick.

[Biojl]

Thanks for the suggestions. I was thinking on NJ because I have thousands of genes. But maybe I'll give it a try to ML and see how quick is it with a constrain.

[DG]

There is also FastTree2 and RAxML-light, both of which can support trees with tens of thousands of taxa or more using some heuristics. FastTree2 is sort of a pseudo-ML but is still quite accurate.