which one is good mafft or clustalW???

Question

[misbahabas]

hello

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

Please tell me which tool is more preferable

Thankx

[microfuge]

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

[GenoMax]

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.

Answer 1

[h.mon]

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.

Answer 2

[bioinfo8]

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.