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

# pxcat(1)

sequence file concatenation

## NAME

pxcat - sequence file concatenation

## SYNOPSIS

**pxcat** \[*OPTIONS*\]... *FILES*

## DESCRIPTION

Sequence file concatenation. Can use wildcards e.g.:

-

  pxcat **-s** \*.phy **-o** my\_cat\_file.fa

### However, if the argument list is too long (shell limit), put filenames in a file:

-

  for x in \*.phy

-

  do echo $x \>\> flist.txt

-

  done

### and call using the -f option:

-

  pxcat **-f** flist.txt **-o** my\_cat\_file.fa

This will take fasta, fastq, phylip, and nexus sequence formats. Individual files may be of different formats.

## OPTIONS

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

  list of input sequence files (space delimited)

- **-f**, **--flist**=*FILE*

  file listing input files (one per line)

- **-p**, **--partf**=*FILE*

  output partition file, none otherwise

- **-u**, **--uppercase**

  export characters in uppercase

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

  output sequence 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