altree-add-Sp - Online in the Cloud

PROGRAM:

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.

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