User:Tara K. Luckau/Notebook/Team ConGen/2012/01/21

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How to FSTAT for FST values and significance

  • spent some time compiling the useful parts of F-statistics output from FSTAT ... here's what I figured out ...
  • FSTAT v

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
20120122 GenePopExcel.png

MS Word

  • copy data from Excel, Paste Special into Word
    • as Unformatted Text
  • Save As ...
    • Plain Text (.txt)
Screen shot 2011-08-18 at 16.12.49.jpg
    • File Conversion: Latin-US (DOS), CR/LF
Screen shot 2011-08-18 at 16.20.04.jpg

Genepop on the Web

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
20120122 GenePop13.png

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
Failed to parse (MathML with SVG or PNG fallback (recommended for modern browsers and accessibility tools): Invalid response ("Math extension cannot connect to Restbase.") from server "":): {\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}}}
20120122 GenePop51.png