drifter

This Perl program simulates genetic drift and sampling error in population genetic samples. It is primarily intended to simulate drift in haploid populations of varying size given known, or predicted, starting conditions (i.e., allele frequencies and times of population origin).

The program was reported in:

Cox MP. 2006. Extreme patterns of variance in small populations: Placing limits on human Y-chromosome diversity through time in the Vanuatu Archipelago. Annals of Human Genetics 71: 390-406.

INSTALLATION

drifter requires a standard working Perl installation and has been confirmed to work with Perl versions up to 5.18.2.

USAGE

For full information, see the complete documentation file.

The following usage assumes a standard installation (i.e., with drifter.pl aliased to drifter).

Basic command line information can be obtained by typing:

drifter

drifter offers a number of command line options:

-b         Verbose – outputs verbose comments
-h         Horizontal – outputs a horizontal format output file
-v         Vertical – outputs a vertical format output file
-t         Timefile – outputs a log file containing run time information
-s         Sampling – creates a sampling profile only for the input populations
-d NUMBER  Seed – allows the user to enter a random number seed
-g NUMBER  Generations – the number of generations for input populations to experience drift
-i NUMBER  Iterations – defines the number of independent replicates

drifter reads information from an input file. The following example, solomons 1, lists the populations to be simulated (here, Malaita and Rendova), their effective population sizes and the sample sizes of the current study, and the names and frequencies of the observed alleles (here, P, K, M and O).

#drifter
poplabel = [Malaita]
Np = [10000]
Ns = [12]
A1 = [K][0.667]
A2 = [S][0.083]
A3 = [M][0.250]
;
poplabel = [Rendova]
Np = [1000]
Ns = [20]
A1 = [K][0.550]
A2 = [O][0.450]
;

At its simplest, drifer is run by invoking the input file:

drifter input.file

EXAMPLE

For details, see the complete documentation file and the example input and output files.

To simulate drift for 10 generations and 2 iterations on the solomons 1 input file, run:

drifter -g 10 -i 2 solomons1.input

drifter of course generates random outcomes, but the output formatting looks like the following, with each block containing the final frequencies of the input alleles for separate simulations after 10 generations of drift:

Number of iterations: 2
Number of generations: 10

K    M    O    S
Malaita    0.58333    0.25000    0    0.16667    
Rendova    0.45000    0    0.55000    0    
;
Malaita    0.75000    0.08333    0    0.16667    
Rendova    0.65000    0    0.35000    0    
;