Phylogenetic inference from binary sequences reduced by primary DNA sequences |
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Authors: | Xiaoqi Zheng Yongchao Dou Jun Wang |
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Institution: | (1) Sabancı University, MDBF, Orhanlı, Tuzla, 34956 İstanbul, Turkey |
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Abstract: | Given a bi-classification of nucleotides, we can obtain a reduced binary sequence of a primary DNA sequence. This binary sequence
will undoubtedly retain some biological information and lose the rest. Here we want to know what kind of and how much biological
information an individual binary sequence carries. Three classifications of nucleotides are explored in the present article.
Phylogenetic trees are built from these binary sequences by the Neighbor-Joining (NJ) method, with evolutionary distance evaluated
on the basis of a symbolic sequence complexity. We find that, for all data sets studied, binary sequences reduced by the purine/pyrimidine
classification give reliable phylogeny (almost the same as that from the primary sequences), while the other two result in
discrepancies at different levels. Some possible reasons and a simple model of sequence evolutionary are introduced to interpret
this phenomenon. |
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