What’s the answer? Open thread

BioStar is a site for asking, answering and discussing bioinformatics questions. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those questions and answers here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

BioStar Question of the Week:

Multiple sequence alignment of thousands of proteins

I want to track the evolution of several domains, and for doing so, I need to align and cluster 1000′s of sequences. is it possible? and what is the best software to use for that? Eventually I want to understand which is the most “basal” sequence that might lead me to the most ancient protein containing this sequence.

–by Dror

The selected answer:

“mafft –auto” is stable for up to hundreds of thousands of proteins and produces reasonable alignments: http://mafft.cbrc.jp/alignment/software/

–by avilella

But there are a couple of other options as well, as with most bioinformatics solutions!  This includes a hot-off-the-press lead on the new Clustal version (Clustal Omega). Check out the others over there.