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BUCKy

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: mbsum and bucky. Loading the BUCKy module on Apocrita enables the use of both of these tools.

  • mbsum summarises the output produced by MrBayes from the analysis of an individual locus.
  • bucky takes the summaries produced by mbsum and performs the second step of BCA.

Usage

To run the latest installed version of BUCKy, simply load the bucky module:

$ 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 bucky --help.

Example job

Serial job

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

Reference