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

# pxcltr(1)

general tree cleaner

## NAME

pxcltr - general tree cleaner

## SYNOPSIS

**pxcltr** \[*OPTIONS*\]...

## DESCRIPTION

General tree cleaner. Removes annotations (node labels), 'knuckles' (2-degree nodes), and root edges to generate a 'vanilla' newick representation. By default removes all properties. Alternatively choose 1 property. This will take a newick- or nexus-formatted tree from a file or STDIN. Output is written in newick format.

## OPTIONS

- **-t**, **--treef**=*FILE*

  input treefile, STDIN otherwise

- **-r**, **--root**

  remove root edge (if present)

- **-l**, **--labels**

  remove internal node labels

- **-k**, **--knuckles**

  remove 2-degree internal nodes

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

  output 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 © 2017-2024 FePhyFoFum License GPLv3