Andrey Zharkikh

TL;DR: A formal mathematical analysis of the substitution process in nucleotide sequence evolution was done in terms of the Markov process by using matrix algebra theory, and it was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 2:191–210, 1987) and Lanave and Hartigan's (Stat. Sci. Sci.) methods are preferable to others for the purpose of phylogenetic analysis when the sequences are long.

TL;DR: To study the evolutionary relationships among the four living gymnosperm orders and the interfamilial relationships in each order, a set of 65 nuclear 18S rRNA sequences from ferns, gymnosperms, and angiosperms was analyzed using the neighbor-joining and maximum-parsimony methods.

TL;DR: Bootstrapping is a conservative approach for estimating the reliability of an inferred phylogeny for four taxa by using model trees of three taxa with an outgroup and by assuming a constant rate of nucleotide substitution.

TL;DR: The complete-and-partial bootstrap technique is proposed as a method for obtaining an unbiased estimate of the confidence level of the monophyly of a particular group of taxa or of an inferred tree topology with the maximum parsimony or neighbor-joining tree reconstruction method.

TL;DR: The results of simulation showed that bootstrap estimation of the confidence level for an inferred phylogeny can be used even under unequal rates of evolution if the rate differences are not large so that the MP method is not misleading.