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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


--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


This program will read the given input file(s) and generate an input file for the phylogenetic reconstruction software paup or phylip/paml ALTREE-CONVERT(1)

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