Comparing multiple sequence alignment programs

Even below the 10-20% identity twilight zone, the best programs correctly align 47% of residues on average

Iterative algorithms are superior, but with a large trade-off in use of computational resources

Global generally performs better than local

No single ‘best’ program exists

For reviews, see:
P. Briffeuil et al., Bioinformatics 1998, 14:357

J. D. Thompson et al., NAR 1999, 27:2682

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