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A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. Although Pseudomarker was originally developed based on the multiple imputation genome scan algorithm, it now includes a comprehensive set of methods. The software package provides a complete workflow in QTL data analysis including data checking and visualization, one, two and multiple QTL model genome scans with covariates, estimating and plotting QTL effect and a variety of plotting and reporting functions. Pseudomarker is specially tailored to work for analyzing large number of phenotypes efficiently, which makes the analysis of eQTL (expression QTL) data possible.

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Pseudomarker classification

Pseudomarker specifications

Software type:
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Programming languages:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
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Pseudomarker distribution


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Pseudomarker support


  • Gary Churchill <>


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The Jackson Laboratory, Bar Harbor, ME, USA

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