PanTools

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.

13
mentions
3
contributors

What PanTools can do for you

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
Keywords
Programming languages
  • Java 99%
  • Snakemake 1%
  • Python 0%
  • Roff Manpage 0%
License
</>Source code
Packages

Participating organisations

Wageningen University & Research
Netherlands eScience Center
SURF

Reference papers

Mentions

Contributors

Thijs van Lankveld
Thijs van Lankveld
Lead RSE
Netherlands eScience Center
EJ
Eef Jonkheer
Researcher
Wageningen University & Research
SS
Sandra Smit
Lead Applicant
Wageningen University

Related projects

Scaling up pangenomics for plant breeding

Delivering a pangenome approach that drastically improves the analytical power on plant data

Updated 1 month ago
Finished

Related software

PanTools-pipeline-v4

PA

General purpose Snakemake pipeline for PanTools v4.

Updated 3 months ago

PanVA

PA

Variant Analysis within Pangenomes.

Updated 3 months ago
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