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Clustal; DNA sequence alignment; Evolutionary distance; Gap character coding; Homology; Indel; Parsimony; Simulation; Tree reconstruction
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How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
How Should Gaps Be Treated In Parsimony? A Comparison Of Approaches Using Simulation, T. Heath Ogden
T. Heath Ogden
Simulation with indels was used to produce alignments where true site homologies in DNA sequences were known; the gaps from these datasets were removed and the sequences were then aligned to produce hypothesized alignments. Both alignments were then analyzed under three widely used methods of treating gaps during tree reconstruction under the maximum parsimony principle. With the true alignments, for many cases (82%), there was no diVerence in topological accuracy for the diVerent methods of gap coding. However, in cases where a diVerence was present, coding gaps as a Wfth state character or as separate presence/absence characters outperformed treating gaps …