Related Experiment Video
Updated: Oct 17, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
PATO: Pangenome Analysis Toolkit
Miguel D Fernández-de-Bobadilla1,2, Alba Talavera-Rodríguez2,3, Lucía Chacón2
1Department of Microbiology, University Hospital Ramón y Cajal, IRYCIS, Madrid, Spain.
Motivation:
We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.
Results:
PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20-30× times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Finally, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.
Availabilityand Implementation:
The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Genomics
Applications of Molecular Taxonomy
Evolutionary Relationships through Genome Comparisons

