Content-type: text/html Man page of MKTEST

MKTEST

Section: User Commands (1)
Updated: May 6, 2002
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NAME

MKtest - a program to calculate nucleotide diversity at silent and replacement sites

SYNOPSIS

MKtest -i <infile> -I <nint> <i,j,k,l,...> -n <samplesize1> [options]

DESCRIPTION

MKtest performs the McDonald-Kreitman test of neutral evolution on full sequence data. The p-value of the test is computed by a Fisher's exact test. The routine for the exact test was lifted from code from the R project (http://www.r-project.org), which in turn is a port of the Fortran FEXACT routine. Where possible, results for G-tests and Chi-squared tests of independence are also output.

OPTIONS

MKtest accepts the following options:

-i <infile>: specify a file containing aligned sequences in FASTA format to analyze
-I <nint> <i j k l...>: specify nint, which is the number of exons you want to analyze. (I.E., nint is the number of coordinates along the sequence you need to specify to describe the beginning and end of every exon). The <i,j,k,l,...> are the coordinates of the start and stop of every exon (please input them in order!!!). If nint is not an even number, and then if the number of positions specified does not equal nint, the program exits with an error message. NOTE: label the exon coordinates starting from 1 (i.e. the first UNGAPPED position in the aligned data is position 1).
-F <posfile>: specify a file name containing the options that you would normally pass to -I
-C <codon_start>: If your exons don't start at a first position, you can tell MKtest what the codon position is of the first exon position. Valid values are 1,2, and 3.
-E <codon_end>: If your exons don't end at a third position, you can tell MKtest what the codon position is of the last exon position. Valid values are 1,2, and 3. -N skip all sites with missing data (the 'N' character).
-n: the number of sequences in the first sample in the data file. For example, if your file contains 20 sequences, 10 from 2 different species, then pass -n 10 as an argument
-A: Provide an approximate treatment of codons in the following cases. First, when there are two substitutions in a codon, and the pathways cannot be unambiguously assigned as silent or replacement, then assume the most conservative pathway (i.e. the one going through at least 1 silent change). Second, when there is a fixed difference between partitions of the data, and all 3 positions are substituted, assign it as a fixed amino acid change if the codons encode different amino acids, else call it a fixed synonymous change.

AUTHOR

Kevin Thornton <k-thornton@uchicago.edu>

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Time: 16:18:46 GMT, August 06, 2003