Johannes de León

Thursday, August 12th, 2004, 07:44 PM

The downloadable zip files located on this page contain software developed at TCGA for the analysis of genetic data, usually in the form of Y chromosome or mtDNA haplotypes. All zip files contain a Word doc help file. Programs were developed on a PC but in many cases can be implemented on other platforms as well. In general, the software has been developed either for Matlab/Octave or R (http://www.r-project.org/)/S-Plus environments.

Currently, the software packages available are:

YTIME (http://www.ucl.ac.uk/tcga/software/Ytime_v204.zip). This is a set of Matlab/R (http://www.r-project.org/) functions to estimate Time to Most Recent Common Ancestor in a clade for which linked microsatellite data are available. The methods assume that the haplotype of the root ancestor is known. This software was first described in Behar et al. (2003), AJHG 73: 768-79

TEST_h_DIFF (http://www.ucl.ac.uk/tcga/software/test_h_diff.zip). This is a set of functions to test for a significant difference in genetic diversity h between two populations, based on samples of haplotypes at a single locus. Both frequentist and Bayesian solutions are presented, and the relative merits discussed. The functions are implemented both in Matlab/Octave and in R (http://www.r-project.org/)/S-Plus. This software was first described in Thomas et al. (2002), AJHG 70: 1411-1420

FLIP (http://www.ucl.ac.uk/tcga/software/FLIP_v200.zip). FLIP stands for “Flexible Likelihood Inference on Populations”. It is made up of a series of Matlab functions that implement the “Monte Carlo Likelihood” method outlined in the paper "Y chromosome evidence for Anglo-Saxon mass migration" by M.E. Weale, D.A. Weiss, R.F. Jager, N. Bradman and M.G. Thomas, Molecular Biology and Evolution 19: 1008-1021.

GenoPheno (http://www.ucl.ac.uk/tcga/software/GenoPheno_v100.zip). This is an R (http://www.r-project.org/) program to run a Monte Carlo method to test departure from expected phenotype levels under the null hypothesis that this is caused by complete association with a fully penetrant binary locus, together with phenotyping error. This method was first described in Mulcare et al. (2004), AJHG 74:1102-1110.

PopA (http://www.ucl.ac.uk/tcga/software/PopA_v200.zip). This is a set of Matlab functions to analyse haplotype frequency data from several populations, calculate statistics that measure the degree of diversity within populations and the genetic distance between populations, and perform bootstrap tests to look for significant differences in these statistics among different populations.

Currently, the software packages available are:

YTIME (http://www.ucl.ac.uk/tcga/software/Ytime_v204.zip). This is a set of Matlab/R (http://www.r-project.org/) functions to estimate Time to Most Recent Common Ancestor in a clade for which linked microsatellite data are available. The methods assume that the haplotype of the root ancestor is known. This software was first described in Behar et al. (2003), AJHG 73: 768-79

TEST_h_DIFF (http://www.ucl.ac.uk/tcga/software/test_h_diff.zip). This is a set of functions to test for a significant difference in genetic diversity h between two populations, based on samples of haplotypes at a single locus. Both frequentist and Bayesian solutions are presented, and the relative merits discussed. The functions are implemented both in Matlab/Octave and in R (http://www.r-project.org/)/S-Plus. This software was first described in Thomas et al. (2002), AJHG 70: 1411-1420

FLIP (http://www.ucl.ac.uk/tcga/software/FLIP_v200.zip). FLIP stands for “Flexible Likelihood Inference on Populations”. It is made up of a series of Matlab functions that implement the “Monte Carlo Likelihood” method outlined in the paper "Y chromosome evidence for Anglo-Saxon mass migration" by M.E. Weale, D.A. Weiss, R.F. Jager, N. Bradman and M.G. Thomas, Molecular Biology and Evolution 19: 1008-1021.

GenoPheno (http://www.ucl.ac.uk/tcga/software/GenoPheno_v100.zip). This is an R (http://www.r-project.org/) program to run a Monte Carlo method to test departure from expected phenotype levels under the null hypothesis that this is caused by complete association with a fully penetrant binary locus, together with phenotyping error. This method was first described in Mulcare et al. (2004), AJHG 74:1102-1110.

PopA (http://www.ucl.ac.uk/tcga/software/PopA_v200.zip). This is a set of Matlab functions to analyse haplotype frequency data from several populations, calculate statistics that measure the degree of diversity within populations and the genetic distance between populations, and perform bootstrap tests to look for significant differences in these statistics among different populations.