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

# pxmono(1)

monophyly checker

## NAME

pxmono - monophyly checker

## SYNOPSIS

**pxmono** \[*OPTIONS*\]...

## DESCRIPTION

Monophyly checker. This will take a newick- or nexus-formatted tree from a file or STDIN.

## OPTIONS

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

  input tree file, STDIN otherwise

- **-n**, **--names**=*CSL*

  names separated by commas (NO SPACES!)

- **-f**, **--namesf**=*FILE*

  names in a file (each on a line)

- **-c**, **--comp**

  take the complement (i.e. check monophyly of taxa not in list)

- **-i**, **--ignore**

  ignore missing (default: exit if names are not in the tree)

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

  output tree 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 © 2019-2024 FePhyFoFum License GPLv3