title: PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD.
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.
authors.affiliation: National Center for Biotechnology Information, NIH, DHHS, Bethesda, MD, USA. gertz@ncbi.nlm.nih.gov.
authors.forename: Edward Michael
authors.initials: EM
authors.lastname: Gertz
authors.forename: Tero
authors.initials: T
authors.lastname: Hiekkalinna
authors.forename: Sébastien Le
authors.initials: SL
authors.lastname: Digabel
authors.forename: Charles
authors.initials: C
authors.lastname: Audet
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Terwilliger
authors.forename: Alejandro A
authors.initials: AA
authors.lastname: Schäffer
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004194:Disease / Q000235:genetics; D005787:Gene Frequency; D008040:Genetic Linkage / Q000235:genetics*; D006801:Humans; D016013:Likelihood Functions; D015810:Linkage Disequilibrium / Q000235:genetics*; D010375:Pedigree; D017422:Sequence Analysis, DNA; D012984:Software