Comparison of phylogenetic trees
1981/02/01 by D.F. Robinson, D. F. Robinson, L.R. Foulds +1 · 2,957 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Biology #Evolution and Paleontology Studies #Evolutionary biology #Gene #Genetic diversity and population structure #Genetics #Genomics and Phylogenetic Studies #Geography #Phylogenetic tree
paper · doi:10.1016/0025-5564(81)90043-2
published in Mathematical Biosciences 53(1-2), 131-147 (Elsevier BV)
openalex publication_date 1981/02/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/06
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