Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
1996/09/01 by Bruce Rannala, Ziheng Yang · 1,674 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #Artificial intelligence #Bayesian probability #Biology #Branching (polymer chemistry) #Branching process #Combinatorics #Computer science #Evolution and Paleontology Studies #Evolutionary biology #Gene #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Inference #Mathematics #Phylogenetic tree #Phylogenetics #Posterior probability #Statistics #Tree (set theory)
paper · doi:10.1007/bf02338839
published in Journal of Molecular Evolution 43(3), 304-311 (Springer Science+Business Media)
openalex publication_date 1996/09/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
Citations
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