Bioinformatics · 2003 · 351 citations · 53 references
Life SciencesBioinformaticsEvolutionary BiologyMolecular EvolutionPhylogeneticsSequence AnalysisDistance-based PhylogeneticsEvolutionary RelationshipsMolecular PhylogenyPhylogenetic AnalysisPhylogenetic Sequence AnalysisPhylogenetic Tree ReconstructionDistance Matrix ConstructionDistance-based PhylogenyDistance-based Tree ReconstructionMolecular Evolutionary ModelsPhylogenetic Distance EstimationPhylogenetic Tree EstimationTree Searching AlgorithmsWhole-genome Phylogeny
Most phylogenetic inference methods rely on multiple sequence alignment and evolutionary models, which fail for some data types such as whole‑genome phylogeny and may be inaccurate. This study introduces a new sequence distance measure based on relative information derived from Lempel–Ziv complexity. The resulting distance matrix is used to construct phylogenetic trees without alignment. The method is fully automatic, does not require alignment, and has produced consistent phylogenies on both real and simulated datasets. The algorithm is available on request from the authors.
Abstract Motivation: Most existing approaches for phylogenetic inference use multiple alignment of sequences and assume some sort of an evolutionary model. The multiple alignment strategy does not work for all types of data, e.g. whole genome phylogeny, and the evolutionary models may not always be correct. We propose a new sequence distance measure based on the relative information between the sequences using Lempel–Ziv complexity. The distance matrix thus obtained can be used to construct phylogenetic trees. Results: The proposed approach does not require sequence alignment and is totally automatic. The algorithm has successfully constructed consistent phylogenies for real and simulated data sets. Availability: Available on request from the authors.
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Julie Thompson, Desmond G. Higgins, Toby J. Gibson · Nucleic Acids Research · 1994 · 64.9K citations · Full text