BayeScan

BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.

Version	module name
2.1	bayescan/2.1

Example Script, available at /share/Apps/examples/bayescan

#!/bin/bash

#SBATCH -p lts
#SBATCH -t 60
#SBATCH -n 20
#SBATCH -N 1

#BayeScan can only be run on a single node

# Load BayeScan module

module load bayesan/2.1

# Set number of OpenMP Threads
export OMP_NUM_THREADS=${SLURM_NTASKS}

cd ${SLURM_SUBMIT_DIR}

bayescan_2.1 test_band_intensity_AFLP.txt
# Want to use different number of threads, say 10
bayescan_2.1 test_binary_AFLP.txt -threads 10
# Use SNP genotypes matrix (See manual for more details)
bayescan_2.1 test_genotype_SNP.txt -snp
# Optional input file (discarded.txt) containing list of loci to discard
bayescan_2.1 test_msats.txt -d discarded

bayescan_2.1 test_SNPs.txt -d discarded.txt -snp -threads 10

For more information visit http://cmpg.unibe.ch/software/BayeScan/