ALTREE-CONVERT

NAME

altree−convert − Title...

SYNOPSIS

altree-convert [options]

 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 (not mandatory)
    −−output−file|o       output file
    −−case−control−output|c  output containing the nb cases/controls
    −−data−type|t         DNA|NUM
    −−phylo−prog|p        PAUP|PHYLIP
    −−reconstruct−prog|r  PHASE|FAMHAP
    −−data−quali|q        Type of data: qualitative or quantitative
    −−nbind−threshold|s   Minimum number of individuals ecquired to keep an haplotype

OPTIONS

−−version

Print the program version and exits.

−−short−help

Print a brief help message and exits.

−−first−input−file|i

Input file 1 (output of the haplotype reconstruction program)

−−second−input−file|j

Input file 2 (second output of famhap or file containig the disease status)

−−output−file|o

Output file

−−case−control−output|c

Output file containing the number of cases and controls carrying each haplotype

−−data−type|t "DNA"|"SNP"

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

−−phylo−prog|p "phylip"|"paup"

Phylogeny reconstruction program

reconstruct−prog|r "famhap|phase"

Haplotype reconstruction program

data−quali|q "qualitative|quantitative"

Type of data analyzed

nbind−threshold|s

Minimal number of individuals carrying an haplotype recquired to keep it for further analysis. If you want to keep all haplotypes, you must affect 0 to this variable

DESCRIPTION

This program will read the given input file(s) and generate an input file for the phylogenetic reconstruction software paup or phylip/paml