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

# pxnj(1)

basic neighbour-joining tree maker

## NAME

pxnj - basic neighbour-joining tree maker

## SYNOPSIS

**pxnj** \[*OPTIONS*\]...

## DESCRIPTION

Basic neighbour-joining tree maker. This will take fasta, fastq, phylip, and nexus inputs from a file or STDIN.

## OPTIONS

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

  input sequence file, STDIN otherwise

- **-n**, **--nthreads**=*INT*

  number of threads, default=1

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

  output newick 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 © 2015-2021 FePhyFoFum License GPLv3