ESTIMATION OF EVOLUTIONARY DISTANCES BETWEEN NUCLEOTIDE-SEQUENCES

A formal mathematical analysis of the substitution process in nucleoti de sequence evolution was done in terms of the Markov process. By usin g matrix algebra theory, the theoretical foundation of Barry and Harti gan's (Stat. Sci. 2:191-210, 1987) and Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984) methods was provided. Extensive computer simulation wa s used to compare the accuracy and effectiveness of various methods fo r estimating the evolutionary distance between two nucleotide sequence s. It was shown that the multiparameter methods of Lanave et al.'s (J. Mol. Evol. 20:86-93, 1984), Gojobori et al.'s (J. Mol. Evol. 18:414-4 22, 1982), and Barry and Hartigan's (Stat. Sci. 2:191-210, 1987) are p referable to others for the purpose of phylogenetic analysis when the sequences are long. However, when sequences are short and the evolutio nary distance is large, Tajima and Nei's (Mol. Biol. Evol. 1:269-285, 1984) method is superior to others.