Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B.

Nature. 2020 Nov;587(7833):246-251. doi: 10.1038/s41586-020-2871-y

Progressive Cactus is a multiple-genome aligner for the thousand-genome era

Aligns with cactus 2~5 genomes, in- and out-group, and reconstitutes an ancestral genome. Recurses the phylogenetic tree progressively. A ‘best-hit-filtering’ step is added to catch duplications that are not seen in the outgroups. Also runs a step ‘removing recoverable chains’ to allow for corrections and mitigate error propagation. Aligning 600 amniotes took ~2 months.