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BMC Bioinformatics. 2014 Feb 17;15:47. doi: 10.1186/1471-2105-15-47.

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD.

Author information

1
National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA. gertz@ncbi.nlm.nih.gov.

Abstract

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.

PMID:
24533837
PMCID:
PMC3932042
DOI:
10.1186/1471-2105-15-47
[Indexed for MEDLINE]
Free PMC Article

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