Gingr visualization of 171 M. tuberculosis genomes aligned with Parsnp. Major clades are visible as correlated SNP densities across the length of the genome.


Whole-genome sequences are now available for many microbial species and clades, however existing whole-genome alignment methods are limited in their ability to perform sequence comparisons of hundreds of sequences simultaneously. Parsnp is a fast core-genome multiple genome aligner that is able to efficiently align thousands of closely related microbial sequences. By only looking at the core-genome, Parsnp can accurately identify core SNPs across all sequences, enabling the reconstruction of large phylogenies of closely related species. Released in 2014, Parsnp is still actively used by the community and maintained by the Treangen lab.


  • Dr. Brian Ondov (NIH)
  • Dr. Sergey Koren (NIH)
  • Dr. Adam Phillipy (NIH)
Todd J. Treangen
Todd J. Treangen
Associate Professor of Computer Science, Bioengineering

My research interests include algorithms and data structures for efficient analysis of microbial genomes and metagenomes

Bryce Kille
Bryce Kille
PhD student

Bryce (2nd year PhD student) received his MS in Bioinformatics and BS in Computer Science + Chemistry from the University of Illinois at Urbana-Champaign. As an undergraduate, he worked at Dow Agrosciences in both the computational biology and cheminformatics groups. His projects included developing software for phylogeny analysis and creating models for compound activity prediction. During his Master’s program, Bryce worked in a biochemistry lab developing software for genome mining as well as a on research project for creating bit-wise algorithms for the C++ STL. One of his main interests is casting biological and chemical problems into theoretical computer science questions.