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Man page of HBKPERMUTE
HBKPERMUTE
Section: User Commands (1)
Updated: April 3, 2002
Index
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NAME
HBKpermute - a program to perform the permutation tests for population substructure described by Hudson, Boos, and Kaplan (1992) Mol. Biol. Evol. 9:138-151.
SYNOPSIS
GSL_RNG_SEED=<seed> HBKpermute -i <infile> -c <config>
[options]
DESCRIPTION
HBKpermute performs a test for population substructure by permuting the population assigments of the sequences in a datafile and calculating a statistic representing the degree of structure observed in the data.
OPTIONS
HBKpermute accepts the following options:
- -i <infile>
-
specify a file containing aligned sequences in FASTA format to analyze
- -c <npop> <config>
-
<config> is a list of numbers representing the sample sizes in each population in the infile, in the order they appear in the infile.
- -O <outgroup>
-
<outgroup> is the index (i.e., counting from zero) of the outgroup sequence in the data, if present
- -n <nperms>
-
number of permutations to run
- -s weight populations by sample size, otherwise they will be weighted equally
-
AUTHOR
Kevin Thornton <k-thornton@uchicago.edu>
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- OPTIONS
-
- AUTHOR
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