MAFFT
Intel Core i5 testing with a Apple MacBook Pro and Intel HD 4000 1536MB on OS X 10.11.1 via the Phoronix Test Suite.
HTML result view exported from: https://openbenchmarking.org/result/1602191-KH-MAFFT551268.
Timed MAFFT Alignment
Multiple Sequence Alignment
Phoronix Test Suite v10.8.4