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altree-convertp - Online in the Cloud

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This is the command altree-convertp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



altree-convert - 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.

--help Print a help message with options descriptions and exits.

--man 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


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

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