Influence of sample variance on the phylogenetic reconstruction of protein sequences
作者： Helena Skutkova , Ivo Provaznik , Rene Kizek
关键词: Phylogenetic reconstruction 、 Mathematics 、 Pattern recognition 、 Phylogenetic tree 、 Phylogenetics 、 Neighbor joining 、 Artificial intelligence 、 Sample variance
摘要: This study deals with the influence of sample variance evolutionary distance estimation on phylogeny reconstruction protein sequences. We modified currently used methods by more precise calculation depending type sequences and model to eliminate this influence.
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sci-hub.st 参考文章(18)
Paul G. Higgs, Teresa K. Attwood, Bioinformatics and Molecular Evolution ,(2005)
Aleksandra Czarna, Rafael Sanjuán, Fernando González-Candelas, Borys Wróbel, Topology testing of phylogenies using least squares methods BMC Evolutionary Biology. ,vol. 6, pp. 105- 105 ,(2006) , 10.1186/1471-2148-6-105
Estimation of evolutionary distance for reconstructing molecular phylogenetic trees. Molecular Biology and Evolution. ,vol. 11, pp. 278- 286 ,(1994) , 10.1093/OXFORDJOURNALS.MOLBEV.A040109
Michael S Rosenberg, Multiple sequence alignment accuracy and evolutionary distance estimation. BMC Bioinformatics. ,vol. 6, pp. 278- 278 ,(2005) , 10.1186/1471-2105-6-278
Toni Gabaldón, Evolution of proteins and proteomes: a phylogenetics approach Evolutionary Bioinformatics. ,vol. 1, pp. 51- 61 ,(2005) , 10.4137/EBO.S0
Yi Zhang, A new model of amino acids evolution, evolution index of amino acids and its application in graphical representation of protein sequences Chemical Physics Letters. ,vol. 497, pp. 223- 228 ,(2010) , 10.1016/J.CPLETT.2010.08.010
Dan Levy, Ruriko Yoshida, Lior Pachter, Beyond Pairwise Distances: Neighbor-Joining with Phylogenetic Diversity Estimates Molecular Biology and Evolution. ,vol. 23, pp. 491- 498 ,(2006) , 10.1093/MOLBEV/MSJ059
John P. Huelsenbeck, Performance of Phylogenetic Methods in Simulation Systematic Biology. ,vol. 44, pp. 17- 48 ,(1995) , 10.1093/SYSBIO/44.1.17
O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution. ,vol. 14, pp. 685- 695 ,(1997) , 10.1093/OXFORDJOURNALS.MOLBEV.A025808
M Nordberg, Metallothioneins: historical review and state of knowledge Talanta. ,vol. 46, pp. 243- 254 ,(1998) , 10.1016/S0039-9140(97)00345-7