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Man page of SHAREDPOLY
SHAREDPOLY
Section: User Commands (1)
Updated: Jun 3, 2002
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NAME
sharedPoly - calculate the number of shared, private, and fixed polymorphisms between 2 partitions of aligned sequence data
SYNOPSIS
sharedPoly -i <infile> -n <sample size of partition 1>
[options]
DESCRIPTION
sharedPoly outputs the number of shared, private, and fixed differences between 2 partitions of aligned sequence data. This may be useful if data are sampled from 2 populations or duplicated genes.
OPTIONS
sharedPoly accepts the following options:
- -i <infile>
-
specify a file containing aligned sequences in FASTA format to analyze
- -h <infile>
-
specify a file containing a polymorphism table in a spreadsheet format
- -n <nsam1>
-
nsam1 is the number of sequences in the first partition. For example, if there are 10 sequences in the file, 6 from population 1, and 4 from population 2, pass -n 6 to the program.
- -b
-
only consider bi-allelic sites in the alignment
- -v
-
verbose output
AUTHOR
Kevin Thornton <k-thornton@uchicago.edu>
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- OPTIONS
-
- AUTHOR
-
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