Incorporating information from length-mutational events into phylogenetic analysis |
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Authors: | Müller Kai |
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Institution: | 1. Anthropology Department, University of Oklahoma, Norman, OK 73019, United States;2. Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73019, United States;3. Electron Microprobe Laboratory, University of Oklahoma, Norman, OK 73019, United States;4. Manitou Springs, CO 80829, United States;5. Ardmore, OK 73401, United States |
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Abstract: | With the growing number of phylogenetic studies that use length variable DNA sequences, incorporating information from length-mutational events into phylogenetic analysis is becoming increasingly important. A new method, modified complex indel coding is described that aims at maximizing the phylogenetic information retained from unambiguously aligned sequence regions or regions where the principal relative position of gaps to one another can be safely established. An algorithm is described that allows application of the method to all theoretically possible gap-nucleotide patterns. A platform-independent computer program is introduced that automates the new method as well as several previously published coding schemes. Differences to previously published indel coding approaches as well as to the integration of ambiguously aligned regions into phylogenetic analysis are discussed. |
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Keywords: | CpDNA DNA sequences Length-mutational events Indel coding Gaps Indels |
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