PanTools version 4.3.1

PanTools is a toolkit for comparative analysis of large number of genomes. It is developed in the Bioinformatics Group of Wageningen University, the Netherlands. Please cite the relevant publication(s) from the list of publications if you use PanTools in your research.


PanTools has been licensed under GNU GENERAL PUBLIC LICENSE version 3.



PanTools currently provides these functionalities:

  • Construction of a panproteome

  • Adding new genomes to the pangenome

  • Adding structural/functional annotations to the genomes

  • Detecting homology groups based on similarity of proteins

  • Optimization of homology grouping using BUSCO

  • Read mapping

  • Gene classification

  • Phylogenetic methods

Running the program

Install PanTools as described in the Installing PanTools page. You can run PanTools from the command line using:

$ pantools <JVM options> <subcommand> <arguments>

Useful JVM options:

  • -Xms<heap size>[unit] : Initial heap size in MB (‘m’) or GB (‘g’)

  • -Xmx<heap size>[unit] : Maximum heap size in MB (‘m’) or GB (‘g’)

  • -XX:StartFlightRecording=filename=<name>.jfr,disk=true : Enable the Flight Recorder (for developers)


All options except for --version also apply to all subcommands.


Display version info.


Display a help message for pantools or any subcommand.


Open the manual for pantools or any subcommand in a local browser.


Force. For instance, force overwrite a database with build_pangenome.


Ignore prompts or any other interactive user input.


Show debug messages in the console.


Only show warnings or higher level logging messages in the console.