---
name: "phipack-profile"
section: "1"
platform: "linux"
package: "phipack"
version: "0.0.20160614-5"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/phipack-profile"
---

# phipack-profile(1)

PHI test and other tests of recombination

## NAME

phipack-profile - PHI test and other tests of recombination

## SYNOPSIS

**Phi** \[*-f\|-s\|-r*\] *Filename*  \[*-t*\] *AlignmentType*

## DESCRIPTION

Input file not specified!!! (use **-f**\|-r\|-s)

-

  \[-w #\] \[-k #\] \[- v\] \[-n #\] \[-m #\]

## OPTIONS

**-f**: Filename = FASTA format

**-s**: Filename = Strict phylip file

**-r**: Filename = Relaxed phylip file

- **-t**: AlignmentType = D\|A\|O where D=DNA

  A=AA and O=OTHER \[default DNA\]

**-w**: # = Change default window size for PHI \[default w = 100\]

**-v**: Verbose \[default = FALSE\]

**-n**: # = Change scanning size for regions to test \[default n = 1000\]

**-m**: # = Step size for profile method \[default m = 25\]