---
name: "pxrecode"
section: "1"
platform: "linux"
package: "phyx"
version: "1.3.2+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pxrecode"
---

# pxrecode(1)

nucleotide sequence recoding

## NAME

pxrecode - nucleotide sequence recoding

## SYNOPSIS

**pxrecode** \[*OPTIONS*\]...

## DESCRIPTION

Nucleotide sequence recoding. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN.

## OPTIONS

- **-s**, **--seqf**=*FILE*

  input sequence file, STDIN otherwise

- **-r**, **--recode**=*STRING*

  string identifying recoding scheme (default: RY)

-

  Supported recodings (use any valid combination):

-

  R = A\|G Y = C\|T S = C\|G W = A\|T M = A\|C K = G\|T B = C\|G\|T D = A\|G\|T H = A\|C\|T V = A\|C\|G

- **-o**, **--outf**=*FILE*

  output sequence file, STOUT otherwise

- **-h**, **--help**

  display this help and exit

- **-V**, **--version**

  display version and exit

- **-C**, **--citation**

  display phyx citation and exit

## CITATION

Brown, Joseph W., Joseph F. Walker, and Stephen A. Smith. 2017. Phyx: phylogenetic tools for unix. Bioinformatics 33(12): 1886-1888. https://doi.org/10.1093/bioinformatics/btx063.

## AUTHOR

Written by Joseph W. Brown

## REPORTING BUGS

Report bugs to: \<https://github.com/FePhyFoFum/phyx/issues\> phyx home page: \<https://github.com/FePhyFoFum/phyx\>

## COPYRIGHT

Copyright © 2013-2024 FePhyFoFum License GPLv3