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

# pxnw(1)

conduct Needleman-Wunsch analysis for all the seqs in a file

## NAME

pxnw - conduct Needleman-Wunsch analysis for all the seqs in a file

## SYNOPSIS

**pxnw** \[*OPTIONS*\]...

## DESCRIPTION

Conduct Needleman-Wunsch analysis for all the seqs in a file. This will take fasta, fastq, phylip, and nexus formats from a file or STDIN. Output is a list of the scores and distances (and the alignments if asked).

## OPTIONS

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

  input sequence file, STDIN otherwise

- **-a**, **--outalnf**=*FILE*

  output sequence file, won't output otherwise

- **-t**, **--seqtype**=*INT*

  sequence type, default=DNA (DNA=0,AA=1)

- **-m**, **--matrix**=*FILE*

  scoring matrix, default DNA=EDNAFULL, AA=BLOSUM62

- **-n**, **--nthreads**=*INT*

  number of threads (open mp), default=2

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

  make the output more verbose, turns off parallel

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

  output score/distance 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 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 © 2013-2024 FePhyFoFum License GPLv3