**SoFoS has moved! Please use the NEW on-line version of SoFoS which can be found here. Please email me if you would like the older perl code referenced below.** Read More...

Tags: libsequence, analysis

COWDUDE (catalogue operation with database user data entry) is a perl script that interfaces with a mysql database to manage germplasm inventory tracking and barcode creation. Read More...

Tags: database

Perl scripts to convert and run Jody Hey's SITES program. Read More...

Tags: fasta, analysis

fastU performs a number of minor fasta-handling utilities Read More...

Tags: fasta

ThetaCurve is a perl script for calculating the a multilocus maximum likelihood value of the per locus Watterson's estimator of the population mutation rate theta. Read More...

Tags: graphing, analysis

A simple perl script that converts files in the .genious format to fasta format.

Runs with the following command:

genious_to_fasta.pl -i

Tags: fasta

RminCutter is a perl script to estimate Hudson & Kaplan's rmin from a standard fasta file, then cut the file into semi-independent regions of sequence with no internal recombination (if you believe that sort of thing). Allows choice of 3 definitions of intervals for output. Read More...

Tags: fasta, analysis

A simple perl script to generate the expected site frequency spectrum for a sample of size n for a population mutation rate of θ. I am no longer entirely sure why you would want to do this. Read More...

Tags: teaching