BEST

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BEST is a Phylogenetics Program design to estimate Phylogenetic Trees

Introduction

BEST, which is an acronym for Bayesian Estimation of Species Trees, is a bioinformatics program designed to analyze phylogenetic trees built out of multilocus molecular sequence data and estimate their joint posterior distributions in a Bayesian framework. This software is designed for use with the MrBayes phylogenetic tree building program. The program can account for deep coalescence but is not designed to address horizontal gene transfer or gene duplication issues among others.

Using BEST on RCC Resources

BEST requires the Intel OpenMPI module to be run on HPC login nodes and on Spear.  In order to load this module, type module load intel-openmpi into the command line interface.

Interactively Running BEST

BEST can be run in a couple of different modes. In order to start an interactive session in BEST, all you need to do is load the necessary module and call BEST from the command line:

module load intel-openmpi
best

Non-Interactive Jobs with BEST

If you want to run BEST non-interactively with a genome file, you can run it on the HPC login nodes or on Spear by running the following commands where EXT is a bioinformatics file format like Nexus (.nex) and FILE is the name of the data file (note that example data files are available on the main website.

module load intel-openmpi
best FILE.EXT

To run BEST non-interactively in parallel ith a genome file, you can run it on the HPC login nodes or on Spear by running the following commands where EXT is a bioinformatics file format like Nexus (.nex) and FILE is the name of the data file (note that example data files are available on the main website.

module load intel-openmpi
mpirun -np 4 best FILE.EXT

Alternatively, you can run BEST in parallel using the Slurm scheduler on multiple nodes. This can be done, for example, with the following slurm script. Again, you can find example data files at the main website.

#! /bin/bash

#SBATCH -J BEST_Testing
#SBATCH -t 01:00:00
#SBATCH -n 4
#SBATCH --mail-type=ALL
#SBATCH -p genacc_q

module load intel-openmpi
mpirun -np 4 best FILE.EXT