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.

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

       --man   Prints the manual page 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