MAFFT Alignment Algorithm
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4.3 years ago
l.souza ▴ 70

Hello,

How trustworthy are the fast MAFFT algorithms (Progressive Methods)? I like using G-INS-i, but now I have to align about 500 sequences and the alignment is extremely slow . I've run the alignment at Galaxy Server, but 15 hours have already passed by and it keeps going.

So, I would like to know if progressive aligments, such as FFT-NS-2, are trustywoth. The alignments are going to be used for phylogenetic analyses.

Thank you in advance!

mafft alignment • 1.7k views
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I would say trustworthy enough, according to here and here (although this paper is now so old its benchmarks are probably meaningless for todays versions). It also depends on how similar your sequences are and size of dataset.

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They are pretty similar! Their size is something between 7 and 8 kilobases

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From my experience it is only a few percent points accuracy difference if you have multiple indels. If you don't, it is probably identical.

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