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.\" ========================================================================
.\"
.IX Title "ALTREE-ADD-S 1p"
.TH ALTREE-ADD-S 1p "2012-10-28" "perl v5.20.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
altree\-add\-S \- Title...
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
altree-add-S [options]
.PP
.Vb 10
\& 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 "?"
.Ve
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-\-version\fR" 8
.IX Item "--version"
Print the program version and exits.
.IP "\fB\-\-short\-help\fR" 8
.IX Item "--short-help"
Print a brief help message and exits.
.IP "\fB\-\-help\fR" 8
.IX Item "--help"
Print a help message with options descriptions and exits.
.IP "\fB\-\-man\fR" 8
.IX Item "--man"
Prints the manual page and exits.
.IP "\fB\-\-first\-input\-file|i\fR" 8
.IX Item "--first-input-file|i"
Input file 1 (paup or phylip file)
.IP "\fB\-\-second\-input\-file|j\fR" 8
.IX Item "--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)
.IP "\fB\-\-output\-file|o\fR" 8
.IX Item "--output-file|o"
Output file
.IP "\fB\-\-epsilon|e\fR" 8
.IX Item "--epsilon|e"
espilon parameter (see formula in the documentation)
.IP "\fB\-\-data\-type|t\fR" 8
.IX Item "--data-type|t"
Type of data: \s-1DNA \s0(\s-1ATGCU\s0) or \s-1SNP \s0(0\-1)
.IP "\fB\-\-proportion|p\fR" 8
.IX Item "--proportion|p"
Proportion of case individuals in the sample
.IP "\fB\-\-outgroup|g\fR" 8
.IX Item "--outgroup|g"
Name of the outgroup (if it is not in the file containing the number of cases and controls per haplotype)
.IP "\fB\-\-data\-qual|q\fR" 8
.IX Item "--data-qual|q"
Specify if the data are qualitative or quantitative
.IP "\fB\-\-low|l\fR" 8
.IX Item "--low|l"
if an haplotype is present equal or less than \-l times, the state of S will be set to \*(L"?\*(R"
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBThis program\fR adds a new character (called \*(L"character S\*(R") to each haplotype in the input file according to the number of cases and controls carrying it.