---
name: "pxaa2cdn"
section: "1"
platform: "linux"
package: "phyx"
version: "1.3.2+ds-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pxaa2cdn"
---

# pxaa2cdn(1)

generate codon alignment from aligned amino acids and unaligned nucleotides

## NAME

pxaa2cdn - generate codon alignment from aligned amino acids and unaligned nucleotides

## SYNOPSIS

**pxaa2cdn** \[*OPTIONS*\]...

## DESCRIPTION

Generate a codon alignment from aligned amino acids and unaligned nucleotides. Taxa found in only 1 input file will be removed. This will take fasta, fastq, phylip, and nexus inputs.

## OPTIONS

- **-a**, **--aaseqf**=*FILE*

  input sequence file, STDIN otherwise

- **-n**, **--nucseqf**=*FILE*

  input sequence file, STDIN otherwise

- **-r**, **--rmlastcdn**

  remove last codon from \*all\* nuc sequences (default: false)

- **-s**, **--stopremove**

  remove stop codon from nuc sequences if present (default: false)

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

  output fasta 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 F. Walker, Joseph W. Brown, Stephen A. Smith (blackrim)

## REPORTING BUGS

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

## COPYRIGHT

Copyright © 2015-2024 FePhyFoFum License GPLv3