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

# pxrlt(1)

taxon relabelling for trees

## NAME

pxrlt - taxon relabelling for trees

## SYNOPSIS

**pxrlt** \[*OPTIONS*\]...

## DESCRIPTION

Taxon relabelling for trees. Two ordered lists of taxa, **-c** (current) and **-n** (new) must be provided. Alternatively, a regex pattern (**-p**) and replacement (**-r**) text can be provided. 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 tree file, STDIN otherwise

- **-c**, **--cnames**=*FILE*

  file containing current taxon labels (one per line)

- **-n**, **--nnames**=*FILE*

  file containing new taxon labels (one per line)

**-p**, **--pattern**=*STRING* regex pattern to replace

**-r**, **--replace**=*STRING* replacement pattern

- **-v**, **--verbose**

  make the output more verbose

- **-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, 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 © 2018-2024 FePhyFoFum License GPLv3