altree-convert1p
Title...
Usage
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
Overview
This program will read the given input file(s) and generate an input file for the phylogenetic reconstruction software paup or phylip/paml
Releases
9 releases since Debian 5.0 (Lenny); the text changed 7 times.