Ellen M. Wijsman: Software and data

• For source code for the MORGAN package or Loki, see The PANGAEA distribution site.
• lnkg2lmm: A Perl script to convert linkage-style files to MORGAN-lm_markers-style files, also distributed from the PANGAEA/MORGAN distribution site.
• Perl scripts for Loki: additional useful scripts for manipulating files from Loki are provided as-is. These are scripts that members of my group have written and that carry out commonly-used tasks. These scripts include computation of Bayes Factors for linkage by uniform intervals or by inter-marker intervals (different from the L-score distributed with Loki); flipping of QTL models to eliminate the model bimodality that is intrinsic in the analysis approach; extracting QTL models that meet particular conditions; and extracting QTL models that fall in an ellipse in a heterozygote-homozygote effect scatter plot. See beginning of each perl script for program documentation.
• SimSuite: A suite of Perl scripts to manage trait simulation from Loki output files, marker simulation, and analysis of results with Loki and/or SOLAR, described by Igo & Wijsman (2008) Empirical significance values for linkage analysis: trait simulation using posterior model distributions from MCMC oligogenic segregation analysis. Genetic Epidemiology 32:119-131. Available very soon (approx Mar. 1, 2008).
• Simulated data used in the paper by Wijsman et al (2006) AJHG 79:846-858 is available at the PANGAEA distribution site.
• Other programs are currently distributed informally, and in a state that is "as is". Contact me if you are interested.