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  운영자 2006-11-13 12:00:05 | Hit : 28334 | Vote : 9090
Subject   [자료] Evolutionary Genetics (Introduction of programs for population genetics)
Evolutionary Genetics (Introduction of programs for population genetics)

야생동물의 개체군유전학에 현재 많이 이용되고 있는 분석프로그램들 중 몇몇 유익한 자료들을 모아보았습니다. IM, SITES, HKA, WH, FPG 등에 대해 간단히 소개하였고 자세한 내용은 링크를 참조하시기 바랍니다.    

IM   - UPDATED 7/31/2006

IM is a program, written with Rasmus Nielsen, for the fitting of an isolation model with migration to haplotype data drawn from two closely related species or populations.  IM is based on a method originally developed by Rasmus Nielsen and John Wakeley (Nielsen and Wakeley 2001 Genetics 158:885).  Large numbers of loci can be studied simultaneously, and different mutation models can be used.  


SITES is a computer program for the analysis of comparative DNA sequence data.  Basic analyses include: data summaries by polymorphism class;  polymorphism estimates within and between groups (species); estimates of migration, neutral model, and recombination parameters; and linkage disequilibrium analyses.  SITES is primarily intended for data sets with multiple closely related sequences. It is especially useful when multiple sequences have been obtained from each of one or several closely related populations or species.  


HKA is a computer program that carries out the widely used statistical test for natural selection that was developed by Hudson, R. R., M. Kreitman and M. Aguadé (1987 A test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159).   This program can handle very large numbers of loci and sample sizes, and conducts tests via coalescent simulation as well as by the conventional chi square approximation.   The simulations can also be used to conduct other tests of natural selection, including tests of Tajima's D statistic (1989) and the D statistic of Fu and Li (1993).


WH is a computer program that carries out the fitting of a speciation model, and conducts tests of the quality of fit of that model.  The speciation model is called the Isolation Model, and is one without gene flow.  With comparative DNA sequence data from each of two closely related species, the method allows an estimation of the time since speciation and the size of the ancestral species.  The methods are described in Wakeley and Hey (1997) and Wang, Wakeley and Hey (1997).


FPG (for Forward Population Genetic simulation) simulates a population of constant size that is undergoing various evolutionary processes, including:  mutation, recombination,  natural selection, and migration.   The meaning of "forward" in this context is simply that time, within the simulation, moves forward just as it does in the real world.  This is in contrast to coalescent population genetic simulation in which time, as represented within the simulation, proceeds back into the past.  Coalescent simulations have many advantages, but they are unwieldy if they incorporate natural selection on multiple sites.

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