NAME

CNDm - Calculate Cytonuclear disequilibrium for multi-allelic systems

SYNOPSIS

CNDm [ -i data input ] [ -o data output ] [ -e log file ] [ -t ] [ -V ] [ -X ] ...

DESCRIPTION

CNDm calculates cytonuclear disequilibria for multi-allelic systems.

OPTIONS

-o

Use this to specify the data output file. CNDm will append to a file that already exists. The default value is CNDm.out.

-i

You need to specify a data input file with this option. The default value is CNDm.dat. See the example files for the format.

-e

This allows you to name a log file. The default value is CNDm.err.

-t

Using this flag flips a switch to output data analysis in LaTeX2e format.

-X

This flag flips a switch to stop the calculation of exact test p-values. It is a way to run a quick analysis.

-V

This is a switch to turn off a bunch of diagnostic messages. The program will run quietly. It is useful for running CNDm as a background job.

-r

This option requires a positive integer and sets the number of repetitions (R) in both the Monte Carlo and Markov chain analyses. If none of the other options are set, then the B parameters will be set to 10 and the C parameters to R/10. It is preferable to use the -rB and -rC options directly. It is zero by default, which means that neither Monte Carlo nor Markov Chain analyses will be performed.

-rB

This requires a positive integer and sets the number of batches of repetitions for both Monte Carlo and Markov Chain analyses. The total number of repetitions is split into batches to estimate sampling variances.

-rC

This requires a positive integer and sets the number of repetitions within a batch for both Monte Carlo and Markov Chain analyses.

-m

This requires a positive integer and sets the number of batches of repetitions for the Markov Chain analysis.

-mB

This sets the number of batches of repetitions forthe Markov Chain analysis.

-mC

This requires a positive integer and sets the number of repetitions within a batch for the Markov Chain analysis.

-M

This requires a positive integer and sets the number of batches of repetitions for the Monte Carlo analysis.

-MB

This sets the number of batches of repetitions forthe Monte Carlo analysis.

-MC

This requires a positive integer and sets the number of repetitions within a batch for the Monte Carlo analysis.

INPUT FORMAT

Your data file should contain cytonuclear counts for multi-allelic systems. The input file is plain text with tokens followed by information that the program will read. A token is any word that begins with a minus sign. Look at the file CNDm.dat as an example of how to format the file.

EXAMPLES

        % CNDm -i sample.dat

Will analyze the data in sample.dat. Analysis follows Asmussen and Basten (1994) and Basten and Asmussen (1997).

        % CNDm -i sample.dat  -rB 100 -rC 1000

Will analyze the dat in sample.dat and do both Monte Carlo and Markov Chain based tests on the data (Basten and Asmussen, 1997). There will be a total of 100,000 repetitions in each Monte Carlo and Markov Chain test, divided into 100 batches of 1,000 repetitions. The program will calculate a p-value and standard error for that p-value for the hypothesis of cytonuclear equilibrium.

REFERENCES

M.A. Asmussen and C.J. Basten (1994). Sampling theory for cytonuclear disequilibria. Genetics 138:1351-1363.
M.A. Asmussen and C.J. Basten (1996). Constraints and normalized measures for cytonuclear disequilibria. Heredity 76:207-214.
C.J. Basten and M.A. Asmussen (1997). The exact test for cytonuclear disequilibria. Genetics 146:1165-1171.

SEE ALSO

CNDd(1)

CONTACT INFO

In general, it is best to contact us via email.

        Christopher J. Basten 
        Bioinformatics Research Center, North Carolina State University
        1523 Partners II Building/840 Main Campus Drive
        Raleigh, NC 27695-7566     USA
        Phone: (919)515-1934
        basten@statgen.ncsu.edu
    
        
The BRC web site ( http://statgen.ncsu.edu/ ) has links to a software page and from there to the 
newest version of this program (Cytonuclear Disequilibria).

The direct link is here: http://statgen.ncsu.edu/brcwebsite/software_BRC.php#Cytonuclear-diseq

There are versions for Windows ( ftp://statgen.ncsu.edu/pub/cnd/CNDWin.zip ), Macintosh ( ftp://statgen.ncsu.edu/pub/cnd/CNDMac.hqx ) and Unix ( ftp://statgen.ncsu.edu/pub/cnd/CNDUnix.tar.gz ).