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altree-add-Sp - Online in the Cloud

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This is the command altree-add-Sp 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-add-S - Title...


altree-add-S [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 data concerning the trait (qualitative or quantitative)
--output-file|o output file
--epsilon|e epsilon value
--data-type|t data type: SNP or DNA
--proportion|p proportion of cases in the sample (for qualitative data only)
--data-qual|q data type: qualitative or quantitative
[--outgroup|g] name of the outgroup
--low|l if an haplotype is present equal or less than -l times, the state of S will be set to "?"


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 (paup or phylip file)

Input file 2, contains the number of times a given haplotypes is carried by case
and control individuals (qualitative data) or the quantitative values
correqsponding to a givent haplotype (quantitative data)

Output file

espilon parameter (see formula in the documentation)

Type of data: DNA (ATGCU) or SNP (0-1)

Proportion of case individuals in the sample

Name of the outgroup (if it is not in the file containing the number of cases and
controls per haplotype)

Specify if the data are qualitative or quantitative

--low|l if an haplotype is present equal or less than -l times, the state of S will be set
to "?"


This program adds a new character (called "character S") to each haplotype in the input
file according to the number of cases and controls carrying it.

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