Man page - altree-convert(1)

Packages contains this manual

Manual

ALTREE-CONVERT

NAME
SYNOPSIS
OPTIONS
DESCRIPTION

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