MAFFT

Question

[QAZ]

Dears,

Why MAFFT is extremely fast comparing to other MSA algorithm? I know it uses FFT algorithm, but that before pairwise alignment. After that, it has steps similar to other MSA algorithms (pairwise alignment, guide tree ..etc)

How is that possible it can run in minutes while other algorithm takes hours!

Thank you in advance.

Answer 1

[Istvan Albert]

I forgot the exact details, but I recall that MAFFT is not an optimal aligner for general use. It is suited to handle certain types of variations. As it says on the page:

https://mafft.cbrc.jp/alignment/software/about.html

The order of alignable blocks or domains are assumed to be conserved for all input sequences.

With examples:

Thus the amazing performance comes at a cost. And you have to understand that there are limitations.

It works extraordinarily well for similar sequences with relatively small variations relative to one another. It does not work well as a generic aligner for more distant sequences. You can consult the benchmarks listed at the link above.

For the record, I agree that MAFFT feels like magic - the speed is unbelievable.