Clustalw: Why Is It Bad That Many Similar Sequences Dominate The Alignment Score?
My book mentioned this as something to be avoided, but I do not understand why.
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This question needs some context. Which book is this, and exactly what does it say? If the relevant section is available on-line, say in Google Books or on similar sites, then link to it so folks can read the relevant section themselves and see what the authors are saying.