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

# pxclsq(1)

clean positions or taxa with too much ambiguous data

## NAME

pxclsq - clean positions or taxa with too much ambiguous data

## SYNOPSIS

**pxclsq** \[*OPTIONS*\]...

## DESCRIPTION

Clean alignments by removing positions/taxa with too much ambiguous data. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN. Results are written in fasta format.

## OPTIONS

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

  input sequence file, STDIN otherwise

- **-p**, **--prop**=*DOUBLE*

  proportion required to be present, default=0.5

- **-e**, **--empty**

  remove columns that are completely empty (- or ?)

- **-m**, **--min**=*INT*

  the minimum number of good characters required per site - a min of 1 is equivalent to **-e** above

- **-t**, **--taxa**

  consider missing data per taxon (default: per site)

- **-c**, **--codon**

  examine sequences by codon rather than site - requires all sequences be in frame and of correct length

- **-i**, **--info**

  report counts of missing data and exit - combine with **-t** to get report by taxon (rather than site) - combine with **-c** to use codons as units

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

  more verbose output (i.e. if entire seqs are removed)

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

  output fasta 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 © 2015-2024 FePhyFoFum License GPLv3