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ALTREE-ADD-S

NAME

altree−add−S − Title...

SYNOPSIS

altree-add-S [options]

 Options:
    −−version             program version
    −−short−help|h        brief help message
    −−help                help message with options descriptions
    −−man                 full documentation
    −−first−input−file|i  input file 1
    −−second−input−file|j input file 2 nb cases/controls per haplotypes
    −−output−file|o       output file
    −−epsilon|e           epsilon value
    −−data−type|t         data type: SNP or DNA
    −−proportion|p        proportion of cases in the sample
    −−ancestor|a          name of ancestral haplotype
    [−−outgroup|g]        name of the outgroup
    [−−low|l]             disease statut for haplotype carried by one individual

OPTIONS

−−version

Print the program version and exits.

−−short−help

Print a brief help message and exits.

−−help

Print a help message with options descriptions and exits.

−−man

Prints the manual page and exits.

−−first−input−file|i

Input file 1 (paup or phylip file)

−−second−input−file|j

Input file 2, contains the number of times a given haplotypes is carried by case and control individuals

−−output−file|o

Output file

−−epsilon|e

espilon parameter (see formula in the documentation)

−−data−type|t

Type of data: DNA ( ATGCU ) or SNP (0−1)

−−proportion|p

Proportion of case individuals in the sample

−−outgroup|g

Name of the outgroup (if it is not in the file containing the number of cases and controls per haplotype)

−−low|l

If this option is present, it forces the state of the character S to be "?" for haplotypes carried by only one individual

DESCRIPTION

This program adds a new character (called "character S") to each haplotype in the input file according to the number of cases and controls carrying it.

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