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.