Scroll to navigation

ALTREE-CONVERT(1p) User Contributed Perl Documentation ALTREE-CONVERT(1p)


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.
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
2020-11-09 perl v5.32.0