Question

which one is good mafft or clustalW???

0

Entering edit mode

6.7 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 • 6.4k views

ADD COMMENT • link updated 6.7 years ago by Biostar 20 • written 6.7 years ago by misbahabas ▴ 70

1

Entering edit mode

Page 44 of t-coffee pdf here provides a detailed comparison.

ADD REPLY • link 6.7 years ago by microfuge ★ 1.9k

1

Entering edit mode

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.

ADD REPLY • link 6.7 years ago by GenoMax 142k

score 0 · Answer 1 · 2017-08-14

0

Entering edit mode

6.7 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.

ADD COMMENT • link 6.7 years ago by h.mon 35k

score 0 · Answer 2 · 2017-08-16

0

Entering edit mode

6.7 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.

ADD COMMENT • link 6.7 years ago by bioinfo8 ▴ 230