分子系統解析 - jst.go.jp
(node) (branch, edge) . (graph). (branch, edge). (node) (leaf), external node . (root). Internal nodes . . (Topology) . . . . A. A C. B. R. C D. B. D. E. Time E. . Operational taxonomic unit (OTU) . . . . outgroup . internal node . . . . . . Newick format Newick format: . 1. 2. 3. 4. 5. . (((1,2),(3,4)),5). Newick format . 2 3 ((1,2),(3,4),5). ((1,2),5),3,4). 4 (1,((3,4),5),2). 1. . 5. . . . . . . . (distance matrix method). (UPGMA). (neighbor joining method, N-J ). (character state method). (maximum parsimony method, MP ). (maximum likelihood method ML ). (Bayesian method) . . . . . UPGMA . . . A. A B C. (AB) C. B dAB B. C d(AB)C. C dAC dBC. C. D d(AB)D dCD. D dAD dBD dCD. D. d(ABC)D. 2. A. A. B. B. C. dAB d(AB)C. 2 2. UPGMA . 1. . 2. . A B ) OTU(AB . . 3. OTU AB . AB dAB . 1. . 2. OTU . 3. . . 1. . 2. . 3. . . Sij . 4. Sij . 2 . 5. OTU . 6. 6. step S12 . 3. 5. 4. Li . . . . L1 + L2 = d12. 3 1 L1 + L3 + L5 = d13. L3 L1. L5. L1 + L3 + L4 = d14.
upgma法（概要） 1. 配列の全ペアから距離行列の計算 2. 距離行列の要素中の最小値をとり、それに対応す る組み合わせ（a、bとする)を1つのotu(ab）とす
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