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Manpage of TOLDHAT
TOLDHAT
Section: User Commands (1)
Updated: April 3, 2002
Index
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NAME
toLDhat - convert a file of FASTA sequences into the set of files
that Gil McVean's program "pairwise" uses to estimate the population
recombination rate.
SYNOPSIS
toLDhat -i <infile> -s <seqfile> -p <posfile>
[options]
DESCRIPTION
toLDhat takes a file of FASTA sequences, a turns it into a seqfile
and a posfile, which are then used by the pairwise program (available
from http://www.stats.ox.ac.uk/~mcvean/LDhat/LDhat.html). toLHhat also
outputs an "infile", which is named after your original file of FASTA sequences,
with the extension ".infile" appended to it. This infile can be redirected into
pairwise to automate the analysis.
OPTIONS
toLDhat accepts the following options:
- -i <infile>
-
specify the filename containing your sequence data in FASTA format
- -s <seqfile>
-
specify the name of the seqfile to write to.
- -p <posfile>
-
specify the name of the posfile to write to
- -b
-
only analyze bi-allelic positions
- -S
-
exclude sites containing singletons
- -g
-
set gene conversion option
AUTHOR
Kevin Thornton <k-thornton@uchicago.edu>
Index
- NAME
-
- SYNOPSIS
-
- DESCRIPTION
-
- OPTIONS
-
- AUTHOR
-
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