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PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD

Edward Michael Gertz1*, Tero Hiekkalinna23, Sébastien Le Digabel4, Charles Audet4, Joseph D Terwilliger256 and Alejandro A Schäffer1

Author Affiliations

1 National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA

2 Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland

3 Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland

4 GERAD and Département de Mathématiques et de Génie Industriel, École Polytechnique de Montréal, Montréal, Canada

5 Department of Psychiatry, Department of Genetics and Development, and Columbia Genome Center, Columbia University, New York NY, USA

6 Division of Medical Genetics, New York State Psychiatric Institute, New York NY, USA

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BMC Bioinformatics 2014, 15:47  doi:10.1186/1471-2105-15-47

Published: 17 February 2014



PSEUDOMARKER is a software package that performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-controls and pedigrees of varying structure into a single unified analysis. Thus it maximizes the full likelihood of the data over marker allele frequencies or conditional allele frequencies on disease and recombination fraction.


The new version 2.0 uses the software package NOMAD to maximize likelihoods, resulting in generally comparable or better optima with many fewer evaluations of the likelihood functions.


After being modified substantially to use modern optimization methods, PSEUDOMARKER version 2.0 is more robust and substantially faster than version 1.0. NOMAD may be useful in other bioinformatics problems where complex likelihood functions are optimized.