I am doing some work that involves comparing different phylogenetic methods and I am having some trouble finding a suitable tool for Bayesian phylogenetics.
I have Geneious and the MrBayes plugin that goes along with it, but it only runs on a single thread and as such is ponderously slow. I have also installed the Linux version of MrBayes along with the extra components needed to use multithreading with it.
The issue with this version of MrBayes is in the fact that it uses a non-standard nexus file format. This is something of a two-fold issue for me. First, the rest of my pipeline uses fasta format and switching file formats back and forth unnecessarily complicates things (and introduces a small chance of accidentally altering the data). Second, the version of nexus used by MrBayes is a non-standard one, which means that none of my existing export tools will adequately handle this.
Is anyone aware of an alternative Bayesian phylogenentics tool? Preferably one that uses fasta?