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