PanTools version 3.4.0
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.
Licence
PanTools has been licensed under GNU GENERAL PUBLIC LICENSE version 3.
Publications
Functionalities
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
Requirements
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 and configuring the required software page.
Running the program
Add the path to the java archive of PanTools, located in the pantools/target subdirectory, to the OS path environment variable. Then run PanTools from the command line by:
$ java <JVM options> -jar pantools-3.4.0.jar <subcommand> <arguments>
Contents
- Installing and configuring the required software
- Construct pangenome
- Pangenome characterization
- Phylogeny
- Multiple Sequence Alignments
- Explore the pangenome
- Read mapping
- Querying the pangenome
- Differences between pangenome and panproteome
- Tutorial 1 - Install PanTools
- Tutorial 2 - Construct pangenome
- Tutorial 3 - Neo4j browser
- Tutorial 4 - Characterization
- Tutorial 5 - Phylogeny
PanTools has its documentation hosted on Read the Docs.