BUCKy is a non-parametric gene and species tree reconciliation application with Bayesian Concordance Analysis (BCA).
BCA works in two steps: First, each locus is to be analysed separately, with MrBayes for instance. Second, all these separate analyses are brought together to inform each other.
BUCKy comes into two separate programs:
bucky. Loading the
BUCKy module on Apocrita enables the use of both
of these tools.
mbsumsummarises the output produced by MrBayes from the analysis of an individual locus.
buckytakes the summaries produced by
mbsumand performs the second step of BCA.
To run the default installed version of BUCKy, simply load the
$ module load bucky $ mbsum --help Usage: mbsum mbsum [--help || -h] [<--skip || -n> number-of-skipped-trees] [<--out || -o> output-file] [--version] [input filename(s)] $ bucky --help Usage: bucky [options] <input files>
For a list of
bucky options, run
Here is an example job running on 1 core and 1GB of memory:
#!/bin/bash #$ -cwd #$ -j y #$ -pe smp 1 #$ -l h_rt=1:0:0 #$ -l h_vmem=1G module load bucky # Read all output from MrBayes and creates a translate section # and a list of tree indicines, trees and their counts. mbsum /path/*.t -o /path/input.in # Perform analysis bucky -o bucky_output_dir \ /path/input.in