altree-convert.1p

Langue: en

Version: 2006-01-10 (debian - 07/07/09)

Section: 1 (Commandes utilisateur)

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|SNP
     --phylo-prog|p        PAUP|PHYLIP
     --reconstruct-prog|r  PHASE|FAMHAP
 
 

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

DESCRIPTION

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