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Online alignment tools? - Are there free programs on the web for multiple alignments? (Dec/02/2006 )


I have used Blast to blast two sequences to align them. But, I have many sequences (several dozen) that I'd like to align.

Are there any tools on the web (free) that you can plug in multiple sequences and have an alignment generated?

We use Sequencher at the lab, but I'd like to do this over the weekend here at home, instead of waiting til Monday.



Quite a number of tools:




and the popular, although not the best, ClustalW:

There is a program called STRAP that serves as a workbench that unites all these programs:


thank you!

Two appear to be specifically for aligning proteins, which is not helpful for my applications (I neglected to specify in my original post). The others look very useful though. I tried MUSCLE and clustal and found MUSCLE to be more what I had in mind.

Much obliged! If I can return the favor in any way (unanswered post or some such you'd like feedback on) please let me know.