Marker Regression Programs are based on marker regression and are designed for detecting covariate effects and interactions from inbred line cross data.

PSEUDOMARKER is a set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. The main theory underlying these programs is presented in Sen and Churchill (2001).

MAANOVA is a set of functions written in Matlab for the analysis of variance on microarray data. These functions are well tested in Matlab R13 for Windows(98/NT4/2000) and Linux Redhat 7.0-8.0. Please note that software on this page is provided for historical continuity but it is no longer actively maintained.  We cannot guarantee that software downloaded from this page will be functional with current releases of R or Matlab.

This software is used to fit Hidden Markov Models in Churchill 1989. Programs are written in C with example input and output.