PanTools version 3

PanTools is a pangenomic 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 mappping
  • 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.

Running the program

Add the path to the java archive of PanTools, located in the /dist/ subdirectory of PanTools project, to the OS path environment variable. Then run PanTools from the command line by:

$ java <JVM options> -jar pantools.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