Good alignment program?

Bernard Murray bernard at elsie.nci.nih.gov
Fri Jan 10 15:45:57 EST 1997


In article <32d60e1d.887692 at news.kth.se>, ev-michael at nrm.se says...
>
>I'm currently using ClustalW 1.5 'big-and-fat' for alignment, but have
>found that it has problems aligning sequences where there are numerous
>(and pretty big) gaps. I'd therefore like to hear what programs other
>people use for alignment - preferrably shareware, but tips about good
>commercial alignment programs is also welcomed.

[snip]

My personal opinion (not yet confirmed by side-by-side testing) is that
ClustalW 1.6 copes with gaps somewhat better than v1.5 so it may be
worth grabbing the later version and giving it a try.  ClustalW is
certainly *much* better than ClustalV at coping with gaps (this I
did confirm by testing).

	Bernard
Bernard Murray, Ph.D.
bernard at elsie.nci.nih.gov (National Cancer Institute, NIH, Bethesda MD, USA)




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