Transcription of 分子系統解析 - jst.go.jp
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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.. 4 L4 L2 2 . S12=L1+L2 L3+L4+L5.. Maximum Parsimony Method (MP ).. 1.
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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