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


  • Java Virtual Machine version 1.8 or higher, Add path to the java executable to your OS path environment variable.

  • KMC: A disk-based k-mer counter, After downloading the appropriate version (linux, macos or windows), add path to the kmc and kmc_tools executables to your OS path environment variable.

  • MCL: The Markov Clustering Algorithm, After downloading and compiling the software, add path to the mcl executable to your OS path environment variable.

For installing and configuring all required software, please see our Installing PanTools page.

Running the program

Make sure you can run java on your command line. Then you can run PanTools from the command line by:

$ java <JVM options> -jar pantools-4.3.1.jar <subcommand> <arguments>
Useful JVM options
- -server : To optimize JIT compilations for higher performance
- -Xmn(a number followed by m/g) : Minimum heap size in mega/giga bytes
- -Xmx(a number followed by m/g) : Maximum heap size in mega/giga bytes


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.