BayeScan

1 Overview | 2 Using | 2.1 Multicore | 2.2 R Functions | 2.2.1 Display of plot_R.r

Overview

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. One of the simplest possible scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient. Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.

Using

Use the module name bayescanto discover versions available and to load the application.

Multicore

The bayescan application allows you define multiple cores with -threads. See bayescan -help for more information.

R Functions

To get the R scripts that come with BayeScan for the installed version:

# Listing the contents of the directory containing the R scripts: For example, on Beartooth:
[]$ ls /apps/u/opt/gcc/12.2.0/bayescan/2.1/R_functions
AFLP_data_functions.r  plot_R.r

To access the R scripts that come with BayeScan for the installed version:

# Copy the folder contatining the R scripts: For example, on Beartooth:
[]$ cp -r /apps/u/opt/gcc/12.2.0/bayescan/2.1/R_functions /directory/to/copy/to

For more details about using the helper scripts refer to the documentation: GitHub - mfoll/BayeScan at v2.1

Display of plot_R.r

If the plot_R.r helper script is run from a node with X11 forwarding enabled from a SSH client that supports it, then the results will be displayed in a X11 window. Otherwise the plot will be saved as a PDF.

Compute nodes do not have X11 forwarding enabled but the Beartooth Login nodes and Beartooth OnDemand GUI desktops do.

To see if the SSH client can display a X11 window:

[@blog1 ~]$  echo $DISPLAY
localhost:11.0

The output of the second line will change depending on the SSH client being used, the important part is that there is output.