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

# altree-convert(1p)

Title...

## NAME

altree-convert - Title...

## SYNOPSIS

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

## DESCRIPTION

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