NAME

       altree - Association and Localisation tests using  phylogenetic Trees

SYNOPSIS

       altree [options]

        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)

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.

       --association|a
               Perform the association test

       --s-localisation|l
               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-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
               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
               test)

       --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-character)

       --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

       --print-tree
               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

DESCRIPTION

       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.