cramb

CIPRES API - MrBayes Submission Client

cramb is a Python 3 application with a GUI built using Tkinter. It is intended to ease the process of sending a Nexus file to CIPRES servers for a bayesian phylogenetic inference (using MrBayes) and then retrieve the results. It assumes your Nexus file has a MrBayes Block correctly configured along with the data to be analysed.

Here is an example of a MrBayes Block inside a Nexus File:

begin mrbayes;
    set autoclose=yes nowarn=yes;
    charset Locus1 = 1-100;
    charset Locus2 = 101-200;
    partition Multi = 2: Locus1, Locus2;
    set partition = Multi;
    lset applyto=(1) nst=6 rates=invgamma;
    lset applyto=(2) nst=6 rates=gamma;
    prset applyto=(2) statefreqpr=fixed(equal);
    outgroup 1;
    mcmc ngen=500000 printfreq=1000 samplefreq=100 nchains=4 temp=0.5 savebrlens=yes;
    sumt relburnin=yes burninfrac=0.25 contype=halfcompat conformat=simple;
END;

More information on the application usage, can be found here.