Based on the results presented herein, all four consistency-based programs Probcons, TCoffee,
Probalign and MAFFT are well recommended for achieving better accuracy at
multiple sequence alignments. Generally, the alignments of Probcons and T-Coffee were
better than Probalign and MAFFT alignments, although the last two programs would be the
most likely choice for datasets of sequences with non-conserved residues at N/C terminal
ends. CLUSTAL OMEGA is also indicated for alignments with non conserved terminal ends.
If high performance computational resources are available, especially with multiple
processing cores, recent versions of MAFFT and T-Coffee can deliver faster alignments
compared to Probalign and Probcons. Parallelization of alignment is a key technique for
increasing speed, which is specially suited for larger datasets than those encountered in the
BAliBASE suite, and should probably be addressed by a higher number of programs in a near