Multiple choice

Which matrix is best suited for phylogenetic analysis?

  1. BLOSUM 80 and PAM 60

  2. BLOSUM 45 and PAM 80

  3. BLOSUM 65 and PAM 250

  4. BLOSUM 30 and PAM 40
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C Correct answer
Explanation

For phylogenetic analysis of distant homologs, matrices designed for detecting remote similarities are needed. BLOSUM 65 (for moderately divergent sequences) paired with PAM 250 (for very distant relationships) provides the best balance of sensitivity and specificity for deep evolutionary comparisons. Lower BLOSUM numbers detect more distant relationships; higher PAM numbers are for more divergent sequences.

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