A substantial update to Clann, the maximum likelihood supertree inference tool. V5.1 introduces proper ML optimality criteria based on Steel & Rodrigo (2008), Robinson–Foulds distance scoring, ML topology tests (Kishino–Hasegawa and Shimodaira–Hasegawa), parallel heuristic search, source-tree weighting schemes, supertree landscape clustering analysis, and a modernised interactive CLI. The codebase has been fully refactored into modular components. The project has been revived after years of dormancy—legacy phylogenetics methods deserve a second life.
This paper addresses a fundamental challenge in multilocus phylogenetics — how to handle cases where different genes cover different subsets of taxa, leading to ineffective overlap. Published in Systematic Biology.
A genomic study of pathogenic Enterobacteriaceae isolated from leafy vegetables, examining antibiotic resistance profiles and the public health implications of resistance gene transfer through the food supply. Published in Environment International.
Troendle, Lee, Reyne et al. (incl. John-Paul Wilkins)
Lab member John-Paul Wilkins contributed to this study demonstrating that combining individual clinical and wastewater whole genome sequencing significantly improves SARS-CoV-2 surveillance. Published in Water Research.
A landmark large-scale study cataloguing previously unexplored microbial diversity across 2,500 food metagenomes and revealing links to the human gut microbiome. Published in Cell.
Chris Creevey co-authored this FAO report on the sustainable use and conservation of rumen microorganisms, highlighting the importance of microbial diversity for efficient and sustainable ruminant digestion. Published by the Food & Agriculture Organisation of the United Nations.
A collaborative study exploring the plant interactions and biogeochemical role of Acidobacteriota — one of the most widespread but poorly understood bacterial phyla in the soil microbiome. Published in Soil Biology and Biochemistry.
Lucy Dillon, Nicholas Dimonaco, Christopher Creevey
Lab members Lucy Dillon, Nick Dimonaco, and Chris Creevey show that accessory genes — those present in some but not all strains of a species — play a defining role in the routes bacteria take towards antibiotic resistance. Published in Life Science Alliance.