A Vector Representation for Phylogenetic Trees

1 code implementation • 11 May 2024 • Cedric Chauve, Caroline Colijn, Louxin Zhang

The HOP distance can be computed in near-linear time, a rare instance of a tree rearrangement distance that is tractable.

The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology

no code implementations • 8 May 2024 • Erin E. Gill, Baofeng Jia, Carmen Lia Murall, Raphaël Poujol, Muhammad Zohaib Anwar, Nithu Sara John, Justin Richardsson, Ashley Hobb, Abayomi S. Olabode, Alexandru Lepsa, Ana T. Duggan, Andrea D. Tyler, Arnaud N'Guessan, Atul Kachru, Brandon Chan, Catherine Yoshida, Christina K. Yung, David Bujold, Dusan Andric, Edmund Su, Emma J. Griffiths, Gary Van Domselaar, Gordon W. Jolly, Heather K. E. Ward, Henrich Feher, Jared Baker, Jared T. Simpson, Jaser Uddin, Jiannis Ragoussis, Jon Eubank, Jörg H. Fritz, José Héctor Gálvez, Karen Fang, Kim Cullion, Leonardo Rivera, Linda Xiang, Matthew A. Croxen, Mitchell Shiell, Natalie Prystajecky, Pierre-Olivier Quirion, Rosita Bajari, Samantha Rich, Samira Mubareka, Sandrine Moreira, Scott Cain, Steven G. Sutcliffe, Susanne A. Kraemer, Yann Joly, Yelizar Alturmessov, CPHLN consortium, CanCOGeN consortium, VirusSeq Data Portal Academic, Health network, Marc Fiume, Terrance P. Snutch, Cindy Bell, Catalina Lopez-Correa, Julie G. Hussin, Jeffrey B. Joy, Caroline Colijn, Paul M. K. Gordon, William W. L. Hsiao, Art F. Y. Poon, Natalie C. Knox, Mélanie Courtot, Lincoln Stein, Sarah P. Otto, Guillaume Bourque, B. Jesse Shapiro, Fiona S. L. Brinkman

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response.

Epidemiology

A Fast and Scalable Method for Inferring Phylogenetic Networks from Trees by Aligning Lineage Taxon Strings

no code implementations • 3 Jan 2023 • Louxin Zhang, Niloufar Abhari, Caroline Colijn, Yufeng Wu

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well.