system, relatedness and genetic distance/diversity programs
updated November 2009
Written by Kermit Ritland
University of British Columbia
MLTR for windows – Version 3.4 (November 2009). This program is described in Ritland (2002 Heredity). Windows version of MLTR, maximum likelihood estimation of mating systems using genetic marker data. Includes methods to characterize biparental inbreeding; allows arbitrary numbers of groups, loci, alleles (described in Ritland 2002). Allows megagametophyte data, dominant markers, genotyping errors, and individual-level estimates with method of moment estimators (dominance not included in this case). Every year or two I have an improvement.
MLTET - estimates multilocus t and F for autotetraploids. I am working on a version for correlated matings. Contact Kermit for more complicated versions of this, which can include apomixes and automixes. Tetraploids do strange things.
MLT - DOS the original multilocus estimation program (for diploids). This is of historical interest.
Mark (I plan to expand this program shortly, and provide adequate documentation. Thanks all for your comments. Due October 2009). This program implements various analyses involving pairwise relatedness and individual inbreeding coefficients, many described in Ritland (2000). Also the current Animal model for association genetics will be incorporated, albeit not a mixed model. The current program implements (1) the procedure for estimating heritability using inferred relatedness, as described in Ritland (1996), (2) isolation by distance analysis and the spatial variance of gene identity (Ritland and Travis 2004), (3) individual inbreeding coefficients and inbreeding genetic load (Ritland and Travis 2004), and just pairwise relatedness. Four alternative measures of relatedness can be used, and these can also be evaluated for your specific data with a Monte Carlo simulation. In addition, a measure of relatedness based upon D-square (mean squared difference of allele size) can also be specified; this is appropriate longer-distance relatedness at microsatellite loci.
GDD and GD - Programs for estimating genetic distance and diversity (GD does standard errors of branch lengths). This is something I wrote a long time ago. Again of historical interest. My two programs now are MLTR for Windows, and Mark (also for Windows). Sorry Mac Guys, but I just program in Fortran.