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

# pxrls(1)

taxon relabelling from alignments

## NAME

pxrls - taxon relabelling from alignments

## SYNOPSIS

**pxrls** \[*OPTIONS*\]... *FILES*

## DESCRIPTION

Taxon relabelling for alignments. This will take fasta, phylip, and nexus formats from a file or STDIN. 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. Results are written in fasta format.

## OPTIONS

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

  input seq 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 © 2016-2024 FePhyFoFum License GPLv3