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altree−add−S − Title...


altree-add-S [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



Print the program version and exits.


Print a brief help message and exits.


Print a help message with options descriptions and exits.


Prints the manual page and exits.


Input file 1 (paup or phylip file)


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


Output file


espilon parameter (see formula in the documentation)


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


Proportion of case individuals in the sample


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


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


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.