MuteBaSS

MuteBaSS (Multi-species Balancing Selection Summary statistics) is a set of Python scripts to perform scans with summary statitics HKA, NCD, NCD_opt, NCD_sub, and NCD_mid, for detecting footprints of long-term balancing selection affecting one or more species (Cheng & DeGiorgio, 2019). Operation of this package requires a UNIX environment with Python 2.7 and above.

Please cite us as:

X. Cheng and M. DeGiorgio. Detection of shared balancing selection in the absence of trans-species polymorphism. 2019. Mol. Biol. Evo. 36(1):177--199

Installation

We distribute MuteBaSS in compressed (tar.gz) format. In addition to the MuteBaSS.py script, we also included the user manual and example data. The scripts included are designed to perform on a UNIX system. To unpack MuteBaSS from the command line, go to the directory where it is stored, and enter

tar -xzvf MuteBaSS.tar.gz
cd MuteBaSS/

Quick Guide

Performing scans

To run MuteBaSS.py, first make sure other python scripts are in the same directory, then format the dash commands and their arguments in a single line as

python MuteBaSS.py -i <input file>  -c <p,x> [--check] [--tree <tree>] [--fixSize] 
    -w <window size> -s <step size> -o <output file> 
    [--NCD] [--tf <tf>] [--NCDopt] [--NCDsub] [--NCDmid]
    [--HKA] [--config <config file>] [--getConfig]

Alternatively, running command python MuteBaSS.py or python MuteBaSS.py -h would return the help page with detailed instructions.

Input format

Input file

The input file should be tab-delimited, and must at least include, in addition to the physical position of each informative site, the number of ancestral alleles (denoted as x) and the total number of alleles sampled (denoted as n). To be an informative site, a site should either be polymorphic in only one of the species examined, or be monomorphically different across all species, with the pattern agreeing with the species tree. Sites that fit neither of these two types should be discarded. All sites should be bi-allelic. All input files should include one-line headers, otherwise the first line will be automatically excluded from analyses. To examine K species, the input file should at least contain the following columns:

position	x1	n1	...	xk	nk

where position is for physical positions, and xj and nj denote the ancestral and total allele counts, respectively, at this position in species j, j = 1, 2, .., K. For this particular input above, the -c <p,x> argument should be -c 1,2.

Here's another example input:

Chr	pos	anc	drv	x1	n1	...	xk	nk

for which the -c <p,x> argument should be -c 2,5.

Configuration file for HKA

When choosing to perform scans with the HKA statistic, users must provide a corresponding configuration file with --config argument. This file records the proportions of within-species polymorphisms and cross-species substitutions for each set of sample sizes among all informative sites (i.e., the two combined) across the genome. Configuration files should not have headers, should be tab-delimited, and each line should present the needed information in the following order in one line:

<n1>	<n2>	...	<nk>	<poly>	<sub>

You can find an example file for 4-species configuration file in the folder test/, which reads:

50	50	50	50	0.283164	0.716836