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stretch coding and block coding: Two new strategies to represent questionably aligned DNA sequences

JOURNAL OF MOLECULAR EVOLUTION 2002年第2期54卷 191-199页

作者： Geiger, DL Santa Barbara Museum Nat Hist Santa Barbara CA 93105 USA

Most coding strategies that address the problem of questionable alignment (elision, case sensitive, missing, polymorphic, gaps as presence/absence matrix) conflict with phylogenetic principles, particularly those relating to the concept of homology (share similiarity explained by common ancestry). In some cases, the test of conjunction is failed. In other cases, characters that are coded ambiguously can lead to character-state optimization in the terminal taxa that conflicts with the original observations. Only data exclusion and contraction avoid these pitfalls. In highly dissimilar sequences additional character states can represent the available information. Two new methods that accomplish this-block and stretch coding-are introduced here. These two new coding strategies are not in conflict with the test of conjunction and do not contradict the original observations. They are comparable to coding practices with morphological data once the intrinsic differences due to character-state identity and topographical identity have been taken into account. It is suggested that, of the three recoding methods, the one is selected that preserves the maximum potential phylogenetic information as measured with the minimum number of steps required for the particular part of the data matrix.

关键词： DNA sequence alignment character coding stretch coding block coding homology test of conjunction

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