One of my coworkers let me know about MAFFT, a multiple sequence alignment program. He thought that it might be useful for my Gsoc project. I found out that it uses a Jalview applet to display the results! Jalview is everywhere! Right now I know that Pfam, Rfam, Clustal, and MAFFT use Jalview applets to display their alignment results...
Addendum: I noticed right after I posted this that one of the alignments in the example file that Jalview has was generated by MAFFT! Shows how observant I am...
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