The
Center for Genetic Anthropology
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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/S-Plus
environments.
FLIP. FLIP stands for Flexible Likelihood Inference on Populations. It is made up of a series of Matlab/Octave 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. This is an R 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. This is a set of Matlab/Octave 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. MantelPartialCorr. This is an R routine to perform Mantel-type permutation testing of the partial correlation of matrix A on B given C. User defines the form of A, B and C. This software was first described in Nadkarni et al. (2005), J Biol Rhythms 20:490-9. TagIT.
This is a set of Matlab routines for selecting and evaluating tagging
SNPs. The most recent version includes automated routines for selecting
tagging SNPs for large candidate gene lists using HapMap data. The
methods implemented in TagIT are described in Weale et al. (2003),
AJHG 73: 551-565, in Goldstein et al. (2003), Trends in Genetics 19:
615-622 and in Ahmadi et al (2005), Nature Genetics 37: 84-89. As
Mike Weale is moving to Duke University, there may be more recent
versions Here.
WinMTSEQreader.zip- This is a WinZip file that contains PC-only stand alone software that takes aligned HVS-1 sequence data in .GDE flat format and produces a list of Variable Sites Only (VSO) for each sample and tentatively groups them into mtDNA haplogroups which can be used to type specific coding region markers as described by Holmquist et al 2006 (in preparation). This software also joins together samples that have been sequenced multiple times. For full description and instructions see readme file within Zip file. It must be extracted using a recent version of WinZip. WinVSOreader.zip-
This is a WinZip file that contains PC-only stand alone software that
takes Variable Sites Only (VSO) lists from HVS-1 sequence data and
tentatively groups samples into mtDNA haplogroups which can be used
to type specific coding region markers as described by Holmquist et
al 2006 (in preparation). For full description and instructions see
readme file within Zip file. It must be extracted using a recent version
of WinZip.
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