MAFFT
Intel Celeron 1017U testing with a Acer Aspire V5-431 and Intel HD 2500 on Ubuntu 14.04 via the Phoronix Test Suite.
HTML result view exported from: https://openbenchmarking.org/result/1503054-SO-MAFFT973416.
Timed MAFFT Alignment
Multiple Sequence Alignment
Phoronix Test Suite v10.8.4