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

# phipack-phi(1)

PHI test and other tests of recombination

## NAME

phipack-phi - PHI test and other tests of recombination

## SYNOPSIS

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

## DESCRIPTION

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

-

  \[-p \[#\]\] \[-o\] \[-v\] \[-g \[#\]\] \[-b \[#\]\]

## 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 \[default DNA\]

**-p**: \[#\] = PHI permutation test \[default = FALSE, #=1000\]

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

**-o**: Report other statistics (NSS and Max Chi^2) \[default = FALSE\]

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

**-g**: \[i\] = Print color (scaled) incompatibility matrix (graph.ppm)

-

  i - Image only (no ticks...) \[default = FALSE\]