If you have several thousand sequences to align, you might want to use
the SAM HMM software:
I often align 10,000 protein sequences using the program, without
I believe SAM has also been used to do rough alignments of 1000s of
1000-long RNA sequences, though HMMs are not good for aligning
structural RNA, as they can't see the important base-pairing signals.
Kevin Karplus karplus at cse.ucsc.eduhttp://www.cse.ucsc.edu/~karplus
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck
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