Deriving Transition Probabilities and Evolutionary Distances from Substitution Rate Matrix by Probability Reasoning
Xuhua Xia · Journal of Genetics and Genome Research · 2017
Substitution rate matrices are used to correct multiple hits at the same sites, which requires the derivation of transition probabilities and evolutionary distances from substitution rate matrices. The derivation is essential in molecular phylogenetics and phylogenomics, and represents the only statistically sound way for developing scoring matrices used in sequence alignment and local string matching (e.g., BLAST and FASTA).