Question: Alternative to MrBayes for BI phylogenetics?
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gravatar for confusedious
4.3 years ago by
confusedious420
Australia
confusedious420 wrote:

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?

ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 4.3 years ago by confusedious420
1

Does MrBayes use a "non-standard" nexus? I thought it was nexus with the option of a "MrBayes block" containing commands? I've always written nexus files for MB with Biopython and had not problems. 

ADD REPLYlink written 4.3 years ago by David W4.7k

Interesting... Maybe it's Geneious that is writing odd nexus files then. I'll take a look at this.

ADD REPLYlink written 4.3 years ago by confusedious420
3
gravatar for apelin20
4.3 years ago by
apelin20470
Canada
apelin20470 wrote:

you can compile mpi version of mrbayes.... there is also phylobayes and beagle/beast

ADD COMMENTlink written 4.3 years ago by apelin20470

I have compiled the MPI version, it runs on mulitple threads fine. It was only the Geneious plug in that doesn't.

I'll check out phylobayes and beagle/beast as well.

ADD REPLYlink written 4.3 years ago by confusedious420
2
gravatar for 5heikki
4.3 years ago by
5heikki8.4k
Finland
5heikki8.4k wrote:

PhyloBayes. There's also a MPI version..

ADD COMMENTlink written 4.3 years ago by 5heikki8.4k
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