---
name: "altree-add-S"
section: "1p"
platform: "linux"
package: "altree"
version: "1.3.2-2+b4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/altree-add-S"
---

# altree-add-S(1p)

Title...

## NAME

altree-add-S - Title...

## SYNOPSIS

altree-add-S \[options\]

```
 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 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 "?"
```

## 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 (paup or phylip file)

- **--second-input-file\|j**

  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\|o**

  Output file

- **--epsilon\|e**

  espilon parameter (see formula in the documentation)

- **--data-type\|t**

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

- **--proportion\|p**

  Proportion of case individuals in the sample

- **--outgroup\|g**

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

- **--data-qual\|q**

  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 "?"

## DESCRIPTION

**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.