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.IX Title "ALTREE 1p"
.TH ALTREE 1p 2024-01-10 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH NAME
altree \- Association and Localisation tests using  phylogenetic Trees
.SH SYNOPSIS
.IX Header "SYNOPSIS"
altree [options]
.PP
.Vb 10
\& Options:
\&    \-\-version        program version
\&    \-\-short\-help|h   brief help message
\&    \-\-help           help message with options descriptions
\&    \-\-man            full documentation
\&    \-\-association|a  perform the association test
\&    \-\-s\-localisation|l   perform the localisation using the S character
\&    \-\-first\-input\-file|i result_file from phylogeny reconstruction programs
\&    \-\-second\-input\-file|j file containing the nb of cases/controls carrying an haplotype
\&    \-\-output\-file|o output_file
\&    \-\-data\-type|t DNA|SNP
\&    \-\-data\-qual|q qualitative|quantitative
\&    \-\-outgroup outgroup_name
\&    \-\-remove\-outgroup 
\&    \-\-tree\-building\-program|p phylip|paup|paml
\&    \-\-splitmode|s nosplit|chi2split
\&    \-\-no\-prolongation
\&    \-\-chi2\-threshold|n value
\&    \-\-permutations|r number
\&    \-\-number\-of\-trees\-to\-analyse number
\&    \-\-tree\-to\-analyse number
\&    \-\-s\-site\-number number
\&    \-\-s\-site\-characters ancestral state \-> derived state
\&    \-\-co\-evo|e simple|double
\&    \-\-print\-tree 
\&    \-\-anc\-seq ancestral sequence (only with phylip)
\&    \-\-nb\-files number of input files to analyse (only for association test)
.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\-\-association|a\fR 8
.IX Item "--association|a"
Perform the association test
.IP \fB\-\-s\-localisation|l\fR 8
.IX Item "--s-localisation|l"
Localise the susceptibility locus using the "S\-character method"
.IP "\fB\-\-first\-input\-file|i\fR \fIresult_file\fR" 8
.IX Item "--first-input-file|i result_file"
Input file 1 (paup, phylip or paml results file).
If several input files are analysed, their names must be separated by colons. 
Example: input1:input2 etc
.IP "\fB\-\-second\-input\-file|j\fR \fIcorrespond_file\fR" 8
.IX Item "--second-input-file|j correspond_file"
Input file 2, default \fIcorrespond.txt\fR.
The number of input file 2 must be the same as the number of input file 1.
The name of the different input file 2 must be separated by colons
.IP "\fB\-\-output\-file|o\fR \fIoutfile\fR" 8
.IX Item "--output-file|o outfile"
Output file
.ie n .IP "\fB\-\-data\-type|t\fR ""DNA""|""SNP""" 8
.el .IP "\fB\-\-data\-type|t\fR \f(CWDNA\fR|\f(CWSNP\fR" 8
.IX Item "--data-type|t DNA|SNP"
Type of data: DNA (ATGCU) or SNP (0\-1)
.ie n .IP "\fB\-\-data\-qual|q\fR ""qualitative""|""quantitative""" 8
.el .IP "\fB\-\-data\-qual|q\fR \f(CWqualitative\fR|\f(CWquantitative\fR" 8
.IX Item "--data-qual|q qualitative|quantitative"
Analyse qualitative (case/control) or quantitative data
.IP "\fB\-\-outgroup\fR  outgroup" 8
.IX Item "--outgroup outgroup"
Root the tree with this outgroup
.IP \fB\-\-remove\-outgroup\fR 8
.IX Item "--remove-outgroup"
Remove the outgroup of the tree before performing the tests
.ie n .IP "\fB\-\-tree\-building\-program|p\fR ""phylip""|""paup""|""paml""" 8
.el .IP "\fB\-\-tree\-building\-program|p\fR \f(CWphylip\fR|\f(CWpaup\fR|\f(CWpaml\fR" 8
.IX Item "--tree-building-program|p phylip|paup|paml"
Phylogeny reconstruction program
.ie n .IP "\fB\-\-splitmode|s\fR ""nosplit""|""chi2split""" 8
.el .IP "\fB\-\-splitmode|s\fR \f(CWnosplit\fR|\f(CWchi2split\fR" 8
.IX Item "--splitmode|s nosplit|chi2split"
how tests are performed from a level to another
.IP \fB\-\-no\-prolongation\fR 8
.IX Item "--no-prolongation"
No prolongation of branches in the tree
.IP "\fB\-\-chi2\-threshold|n\fR value" 8
.IX Item "--chi2-threshold|n value"
Significance threshold for chi2 (default value 0.01)
.IP "\fB\-\-permutations|r\fR number" 8
.IX Item "--permutations|r number"
Number of permutations used to calculate exact p_values
(Only for association test)
.IP "\fB\-\-number\-of\-trees\-to\-analyse\fR number" 8
.IX Item "--number-of-trees-to-analyse number"
Number of trees to analyse in the localisation analysis 
(only for localisation method using S\-character)
.IP "\fB\-\-tree\-to\-analyse\fR number" 8
.IX Item "--tree-to-analyse number"
With this option, you can specify the tree to use (instead of
random). Can be used several times to specify multiple trees.
.IP "\fB\-\-s\-site\-number\fR number" 8
.IX Item "--s-site-number number"
Number of the S character site in the sequence
(only for localisation method using S\-character)
.IP "\fB\-\-s\-site\-characters\fR transition" 8
.IX Item "--s-site-characters transition"
Character states for the S character: ancestral state \-> derived state
ex: G\->C or 0\->1  (only for localisation method using S\-character)
.ie n .IP "\fB\-\-co\-evo|e\fR ""simple""|""double""" 8
.el .IP "\fB\-\-co\-evo|e\fR \f(CWsimple\fR|\f(CWdouble\fR" 8
.IX Item "--co-evo|e simple|double"
Type of co-evolution indice 
  simple: only the anc \-> der transition of S is used 
  double: the two possible transitions are used
.IP \fB\-\-print\-tree\fR 8
.IX Item "--print-tree"
If this option is selected, the tree will be printed to the output
.IP "\fB\-\-anc\-seq\fR anc_seq" 8
.IX Item "--anc-seq anc_seq"
With this option, you can specify the ancestral sequence.
This option is only useful when the tree is reconstructed using the mix program 
of phylip with the ancestral states specified in the file "ancestors"
.IP "\fB\-\-nb\-files\fR number" 8
.IX Item "--nb-files number"
With this option, you specify the number of input files (1 and 2)  to analyse
This option only works for the association test. Be careful if the number of trees is not
the same for the different input files: if the chosen tree doesn't exist in one file, 
the program wil not work correctly
.SH DESCRIPTION
.IX Header "DESCRIPTION"
\&\fBThis program\fR performs
.PP
(a) an association test between a candidate gene and disease or a quantitative trait
.PP
(b) a localsation tests: it allows to detect which SNP is involved in the determinism of the disease or the quantitative trait
.PP
These two tests are based on the analysis of haplotype phylogenetic trees.