altree-convert(1) Title...


altree-convert [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


Print the program version and exits.
Print a brief help message and exits.
Print a help message with options descriptions and exits.
Prints the manual page and exits.
Input file 1 (output of the haplotype reconstruction program)
Input file 2 (second output of famhap or file containig the disease status)
Output file
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
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


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