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altree - Association and Localisation tests using phylogenetic Trees


altree [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
--tree-building-program|p phylip|paup|paml
--splitmode|s nosplit|chi2split
--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
--anc-seq ancestral sequence (only with phylip)
--nb-files number of input files to analyse (only for association test)


Print the program version and exits.

Print a brief help message and exits.

--help Print a help message with options descriptions and exits.

--man Prints the manual page and exits.

Perform the association test

Localise the susceptibility locus using the "S-character method"

--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

--second-input-file|j correspond_file
Input file 2, default correspond.txt. 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

--output-file|o outfile
Output file

--data-type|t "DNA"|"SNP"
Type of data: DNA (ATGCU) or SNP (0-1)

--data-qual|q "qualitative"|"quantitative"
Analyse qualitative (case/control) or quantitative data

--outgroup outgroup
Root the tree with this outgroup

Remove the outgroup of the tree before performing the tests

--tree-building-program|p "phylip"|"paup"|"paml"
Phylogeny reconstruction program

--splitmode|s "nosplit"|"chi2split"
how tests are performed from a level to another

No prolongation of branches in the tree

--chi2-threshold|n value
Significance threshold for chi2 (default value 0.01)

--permutations|r number
Number of permutations used to calculate exact p_values (Only for association

--number-of-trees-to-analyse number
Number of trees to analyse in the localisation analysis (only for localisation
method using S-character)

--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.

--s-site-number number
Number of the S character site in the sequence (only for localisation method using

--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)

--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

If this option is selected, the tree will be printed to the output

--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"

--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


This program performs

(a) an association test between a candidate gene and disease or a quantitative trait

(b) a localsation tests: it allows to detect which SNP is involved in the determinism of
the disease or the quantitative trait

These two tests are based on the analysis of haplotype phylogenetic trees.

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