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Man page of GESTIMATOR
GESTIMATOR
Section: User Commands (1)
Updated: April 3, 2002
Index
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NAME
gestimator - The "GNU estimator" (pronounced guesstimator) is a program to calculate divergence between coding sequences
SYNOPSIS
gestimator -i <infile>
[options]
DESCRIPTION
The primary function of gestimator calculates nonsynonymous (Ka) and synonymous (Ks) distances between DNA sequences, using Comeron's method (Comeron, J. (1995) J. Molecular Evolution, 41: 1152-1159). To keep all the output numeric, the value '999' may be reported if the divergence calculation cannot be made. The program will do all pairwise comparisons for a file containing more than 2 sequences
OPTIONS
gestimator accepts the following options:
- -i <infile>
-
specify a file containing aligned sequences in FASTA format to analyze
- -v
-
verbose output. See Comeron's paper for an explanation of the variables.
- -m <maxhits>
-
maxhits is an int referring to the maximum number of differences between two aligned codons to analyze. Accepted values are 1,2, or 3.
- -g
-
remove gaps from the whole aligment before doing any calculations. The default behavior is to remove the gaps from each pairwise comparison.
AUTHOR
Kevin Thornton <k-thornton@uchicago.edu>
Index
- NAME
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- SYNOPSIS
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- DESCRIPTION
-
- OPTIONS
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- AUTHOR
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