PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD
Related Experiment Video
Updated: May 3, 2026

A Psychophysics Paradigm for the Collection and Analysis of Similarity Judgments
Published on: March 1, 2022
Edward Michael Gertz1, Tero Hiekkalinna, Sébastien Le Digabel
1National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA. gertz@ncbi.nlm.nih.gov.
Background:
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.
Results:
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.
Conclusions:
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.
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