IQ-TREE

IQ-TREE is a high-throughput phylogenetic tree software capable of handling multiple sequence alignment files. It reconstructs the evolutionary tree as best explained by the data. Note it will throw an error if the exons are not divisible by 3.

For additional information and examples see the documentation

ml biocontainers iqtree
iqtree -s input.phy

Parallel Capabilities: Single core default, Multithreading options supported.