Is it better to use MUSCLE or CLUSTALW to align amino acid sequences of proteins belonging to the same superfamily?
out of those two, use MUSCLE
If your superfamily is in SUPERFAMILY (http://supfam.org) you can use the HMM alignment tool for domain alignments.
As Julian Gough said, out of these 2 programs, go for MUSCLE.
ClustalW implements an iterative algorithm so mistakes produce in earlier step are quite unlikely to be corrected in later step meanwhile muscle implements an progressive algorithm allowing re-optimizations of columns during the whole process.
I'd recommend to give a try to MAFFT if you are looking for programs as fast as MUSCLE with a variety of algorithms depending on how many sequences you have. An alternative is T-Coffee, slower than Mafft or Muscle but with really good performance.
Hi. For my opinion, MUSCLE is better for Amino Acid Aligning than ClustralW.
I also have the same question to Manan Vishvas Desai.
Thanks all.
Thanks to Taghi Ghassemi-Khademi.
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