Good alignment program?

Bernard Murray bernard at
Fri Jan 10 15:45:57 EST 1997

In article <32d60e1d.887692 at>, ev-michael at 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.


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 Murray, Ph.D.
bernard at (National Cancer Institute, NIH, Bethesda MD, USA)

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