Welcome to the FREQ Seq Site

FREQ Seq is a method that allows one to accurately, rapidly and cheaply measure allele frequencies in genetic samples from populations using Illumina sequencing and a protocol recently described in Chubiz, Lee, Delaney and Marx.

This page provides software for doing the analysis of the FastQ files that are produced by the Illumina sequencing step.  This program quickly converts the large sequence files by aligning and assigning the reads from them to create simple summary files that can be analyzed and plotted in R, SAS, Excel, JMP, Python or other software.

The program can process and assign a terabyte of data in less than 20 seconds while using under 75 MB of RAM on our test machine with a standard i7 processor.  It does not require the user to re-compile anything.