Canopy is a new method for co-estimation of phylogeny and phylogeny-aware sequence alignment. Canopy is built on top of PRANK and allows splitting the progressive alignment into subproblems, computing these separately and then merging the subalignments into a full multiple alignment. Canopy incorporates several methods for phylogeny inference and provides different strategies for iterative co-estimation of alignment and phylogeny. Canopy can parallelise the task across multiple CPU-cores and thus efficiently utilise modern computer hardware.
Research topic: Canopy — parallelised, iterative search of optimal phylogeny and phylogeny-aware MSA
