Re: [DIYbio] Favorite Tools for Aligning Multiple Sequences

Alright, so you're doing multiple sequence alignments? Like, global alignments?

Finally, a chance for me to be useful. I don't do synthetic biology, but I am interested in evolution, and, unsurprisingly, multiple alignment is very, very important to molecular phylogenetics-- if your alignment is no good, your phylogenetic reconstruction will be no good. However, picking an alignment method isn't that easy; "The Phylogenetic Handbook" lists, IIRC, some 43 different alignment algorithms. They take fundamentally different approaches, too; my favorite, which seems somehow thematically appropriate, is that of genetic algorithms.

"The Phylogenetics Handbook" has this to say about Clustal:

> Although ClustalW is still the most popular alignment tool, several more recent methods have now been shown to perform better in terms of accuracy and/or speed.


It has a nice table under the "Which program to choose?" section. You're probably in the realm of the first case:

> Input data: 2-100 sequences of typical protein length (maximum 10,000 residues) that are approximately globally alignable
>
> Recommendations: Use ProbCons, T-Coffee, and MAFT or MUSCLE, compare the results using AltAVisT. Regions of alignment are more likely to be correct. For sequences with low percent identity, ProbCons is generally the most accurate, but incorporating structure information (where available) via 3DCoffee (a variant of T-Coffee) can be extremely helpful.

Personally, I tend to use T-Coffee. The tradeoff here is between accuracy and computational requirements: T-Coffee is generally more accurate, but Clustal has lower memory requirements. I think Clustal is currently in the realm of "everyone uses it because everyone else uses it".

I'm no expert, either, so take this with the requisite grain o' salt.

--T.

On Jun 25, 2012, at 5:27 PM, L wrote:

> Hey there everyone,
> I'm looking for a way to quickly create protocols for transformation of artificial yeast chromosomes. Got lots of ideas, the means to try them all, and now I'm just looking into what restriction enzymes I'll need. Confused by BLAST, any help using that would be awesome.
>
> Thank you!
>
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