Proposal Summary
To significantly speed up IQ-TREE to enable real-time genomic epidemiology during ongoing outbreaks such as COVID-19, and to introduce continuous integration and a testing framework to ease software maintenance for all developers.
IQ-TREE
IQ-TREE is a widely-used open source software tool in biomedical sciences. The original IQ-TREE paper has been cited over 6,800 times and the software has been downloaded over 50,000 times in 2020. IQ-TREE reconstructs phylogenetic trees from DNA sequence data, allowing users to understand evolutionary histories of viruses, bacteria, animals, plants, and all organisms. Notably, IQ-TREE has recently been instrumental in tracking the variants of the novel coronavirus (SARS-CoV-2) and identifying key mutations. This provides crucial information for contact tracing, understanding public health measures, and designing new vaccines. This proposal aims to extend IQ-TREE to a new real-time phylogenetics paradigm suitable for the new era of genomic epidemiology by significantly speeding up IQ-TREE by developing real-time algorithms that allow continuous updates of phylogenetic trees with millions of genomes.