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altree − Analysing phylogeny 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
    −−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)



Print the program version and exits.


Print a brief help message and exits.


Print a help message with options descriptions and exits.


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)

−−second−input−file|j correspond_file

Input file 2, default correspond.txt

−−output−file|o outfile

Output file

−−data−type|t "DNA"|"SNP"

Type of data: DNA ( ATGCU ) or SNP (0−1)

−−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


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)


Character states for the S character: ancestral state −> derived state ex: G−>C or 0−>1 (only for localisation method using S−character)


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


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"


This program will read the given input file(s) and do someting useful with the contents thereof.