which one is good mafft or clustalW???
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6.8 years ago
misbahabas ▴ 70

hello

which tool is good for multiple sequence alignment of genes sequences Mafft or clustalW??

Please tell me which tool is more preferable

Thankx

alignment blast genome • 6.5k views
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Page 44 of t-coffee pdf here provides a detailed comparison.

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MSA programs are going to get you part way to the end. At some-point you are going to need to examine/edit/adjust the alignment manually so it makes the best sense.

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6.8 years ago
h.mon 35k

ClustalW algorithm is quite old and has been supplanted (speed and precision) by several others - MAFFT among them, but also Muscle and T-Coffee, for example. EBI web services does not provide ClustalW anymore - it has ClustalOmega, which they recommend for protein alignments.

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6.8 years ago
bioinfo8 ▴ 230

My first preference is always ClustalX (for more sequences) and Clustal Omega (for few sequences). For extensive analysis, MEGA is awesome.

But, one should always try to use 2 or more tools to validate the output.

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