Pseudomarker [Joint Linkage and/or Linkage Disequilibrium Analysis]
Version 2.0

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PSEUDOMARKER is linkage analysis software for joint Linkage and LD analysis for qualitative traits. PSEUDOMARKER code is written by Tero Hiekkalinna, Joseph D. Terwilliger and Petri Norrgrann. FASTLINK 4.1P code is written by Alejandro A. Schäffer, E. Michael Gertz and others. NOMAD code is written by Sébastien Le Digabel, Charles Audet and others.

PSEUDOMARKER can analyze different data structures jointly such as cases and controls, trios, sib pairs, sib ships and extended families. Pseudomarker is a family-based association test.

"Don't make your data fit the analysis method, make the analysis method fit your data!"

PSEUDOMARKER version 2.0 using FASTLINK4.1P/NOMAD released 27th of February, 2014!

Version 2.0 is released!

A Mac OS X version is available as well!

PSEUDOMARKER 2.0 uses a special version of ILINK program (FASTLINK4.1P package) that uses NOMAD optimization software to maximize likelihoods. Analyses are significantly faster! NOMAD stands for Nonlinear Optimization by Mesh Adaptive Direct Search. NOMAD software site is:

Latest publication:

PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD. E. Michael Gertz, Tero Hiekkalinna, Sébastien Le Digabel, Charles Audet, Joseph D. Terwilliger and Alejandro A. Schäffer. BMC Bioinformatics 2014, 15:47 (Link to article)

See also:

Hiekkalinna, T. (2012). On the superior power of likelihood-based linkage disequilibrium mapping in large multiplex families compared to population based case-control designs. Ph.D. thesis, University of Helsinki, Helsinki, Finland. Online PDF:

PSEUDOMARKER: A powerful program for joint linkage and/or linkage disequilibrium analysis on mixtures of singletons and related individuals. T. Hiekkalinna, A. A. Schäffer, B. W. Lambert, P. Norrgrann, H.H.H. Göring, J.D. Terwilliger. Human Heredity 2011;71:256-266 (Link to article).

On the statistical properties of family-based association tests in datasets containing both pedigrees and unrelated case-control samples. T. Hiekkalinna, H.H.H. Göring, B. W. Lambert, K. M. Weiss, P. Norrgrann, A. A. Schäffer, J.D. Terwilliger. European Journal of Human Genetics 2012 Feb;20(2):217-23. (Link to article).

On the validity of the likelihood ratio test and consistency of resulting parameter estimates in joint linkage and linkage disequilibrium analysis under improperly specified parametric models. T. Hiekkalinna, H.H.H. Göring, J.D. Terwilliger. Annals of Human Genetics 2012 Jan;76(1):63-73. (Link to article)

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