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 data concerning the trait (qualitative or quantitative)
           --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 (for qualitative data only)
           --data-qual|q         data type: qualitative or quantitative
           [--outgroup|g]        name of the outgroup
           --low|l               if an haplotype is present equal or less than -l times, the state of S will be set to "?"

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 (qualitative data) or the quantitative values
               correqsponding to a givent haplotype (quantitative data)

       --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)

       --data-qual|q
               Specify if the data are qualitative or quantitative

       --low|l if an haplotype is present equal or less than -l times, the state of S will be set
               to "?"

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.