---
name: "psort"
section: "1"
platform: "linux"
package: "psortb"
version: "3.0.6+dfsg-4+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/psort"
---

# psort(1)

bacterial localization prediction tool

## NAME

psort - bacterial localization prediction tool

## SYNOPSIS

**psort** \[*-p\|-n*\] \[*OPTIONS*\] \[*SEQFILE*\]

## DESCRIPTION

Runs psort on the sequence file SEQFILE .  If SEQFILE isn't provided then sequences will be read from STDIN.

- **--help**, **-h**

  Displays usage information

- **--positive**, **-p**

  Gram positive bacteria

- **--negative**, **-n**

  Gram negative bacteria

- **--archaea**, **-a**

  Archaea

- **--cutoff**, **-c**

  Sets a cutoff value for reported results

- **--divergent**, **-d**

  Sets a cutoff value for the multiple localization flag

- **--matrix**, **-m**

  Specifies the path to the pftools installation.  If not set, defaults to the value of the PSORT\_PFTOOLS environment variable.

- **--format**, **-f**

  Specifies sequence format (default is FASTA)

- **--exact**, **-e**

  Skip SCLBLASTe (useful for batch runs of data against itself in SCLBLAST)

- **--output**, **-o**

  Specifies the format for the output (default is 'normal'  Value can be one of: terse, long or normal

- **--root**, **-r**

  Specify PSORT\_ROOT for running local copies.  If not set, defaults to the value of the PSORT\_ROOT environment variable.

- **--server**, **-s**

  Specifies the PSort server to use

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

  Be verbose while running

**--x-skip-localization**

- **--version**

  Print the version of PSortb

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.