[BioC] can I use alignment utilities (mismatchTable, etc) on externally-generated alignments?

Janet Young jayoung at fhcrc.org
Wed Oct 10 03:49:23 CEST 2012

Hi there,

I've been trying to figure out whether I can use some of your very nice alignment utilities (e.g. mismatchTable) on pairwise alignments I've generated in other ways than pairwiseAlignment?  For example, alignments I've generated using programs outside of R, and then read in using readDNAMultipleAlignment or readDNAStringSet.

I've been poking around a bit and can't see a way to do it, but I might be missing something - maybe there's some kind of coercion I should do?

If there isn't a way to run mismatchTable on outside alignments, can I put in a plug for it - it'd be really useful for me, at least.

thanks very much,



Dr. Janet Young 

Tapscott and Malik labs

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung  ...at...  fhcrc.org


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