altree-convertp - Online in the Cloud

PROGRAM:

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

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