User:Tara K. Luckau/Notebook/Team ConGen/2012/01/22

Tara's Lab Notebook

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How to GENEPOP for Hardy-Weinberg Equilibrium Spent some time today and in past figuring out how Genepop works ... here's what I figured out ... Genepop 4.0.10, Genepop on the Web Formatting Data MS Excel first row can be anything (title your Genepop run, for example) second row is marker names, separated by commas third row is lthe word "POP" (or "Pop" or "pop"), to separate populations fourth row is data start with sample name - can use any character, including white space comma genotypes separated by white space MS Word copy data from Excel, Paste Special into Word as Unformatted Text Save As ... Plain Text (.txt) File Conversion: Latin-US (DOS), CR/LF Genepop on the Web http://genepop.curtin.edu.au/ Option 1: Hardy Weinberg Exact Tests Suboption 3: Probability Test will output Hardy-Weinberg chi-square test, along with significance grouped by marker grouped by population overall Option 5: Allele Frequencies, etc. Suboption 1: Genotypic matrices, number obs/exp homozygotes and heterozygotes, allele frequencies, etc will output genotype matrix (how often one allele occurs with another), genotype frequences, expected and observed number of homozygotes and heterozygotes, allele frequences calculate He and Ho [math]\displaystyle{ H_e = \tfrac{\mbox{expected number of heterzygotes}}{\mbox{number of samples}}\mbox{ . . . }H_o = \tfrac{\mbox{obvserved number of heterzygotes}}{\mbox{number of samples}} }[/math]