phylonium

phylonium is a software tool that efficiently and accurately computes pairwise distances between large sets of closely related genome sequences, such as those collected during disease outbreak tracking using whole-genome sequencing. The key features and improvements of phylonium are:

1. Indexing: Unlike its predecessor, which indexed each sequence, phylonium achieves similar accuracy by indexing only a single sequence, significantly reducing the indexing time.

2. Speed: Phylonium is approximately 100 times faster than its predecessor when applied to a dataset of 2,678 Escherichia coli genomes from ENSEMBL.

3. Accuracy: Despite the faster processing time, phylonium maintains a level of accuracy comparable to its predecessor.

4. Comparison to other tools: While mash, one of the best-published programs for rapidly computing pairwise distances, analyzes the same dataset four times faster than phylonium, it is less accurate than phylonium when using default settings.