Cladistics · 1996 · 523 citations · 8 references
Life SciencesBioinformaticsEvolutionary BiologyMolecular EvolutionPhylogeneticsSequence AnalysisPhylogenetic AnalysisPhylogenetic PatternsPhylogenetic Sequence AnalysisPhylogenetic Tree ReconstructionPhylogenomic AnalysisSequence AlignmentAlignment OptimizationDeletion EventsDna Sequence AnalysisMultiple Sequence AlignmentParsimony-based ReconstructionPhylogenetic Character OptimizationPhylogenetic Tree Topology InferenceTree Searching Algorithms
Abstract— A method is described to assess directly the number of DNA sequence transformations, evolutionary events, required by a phylogenetic topology without the use of multiple sequence alignment. This is accomplished through a generalization of existing character optimization procedures to include insertion and deletion events (indels) in addition to base substitutions. The crux of the model is the treatment of indels as processes as opposed to the patterns implied by multiple sequence alignment. The results of this procedure are directly compatible with parsimony‐based tree lengths. In addition to the simplicity of the method, it appears to generate more efficient (simpler) explanations of sequence variation than does multiple alignment.
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