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Neighbour joining method

Neighbour joining method. The neighbor joining method is a greedy heuristic which joins at each step, the two closest sub-trees that are not already joined It is based on the minimum evolution principle

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Neighbour joining method

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  1. Neighbour joining method • The neighbor joining method is a greedy heuristic which joins at each step, the two closest sub-trees that are not already joined • It is based on the minimum evolution principle • One of the important concepts in the NJ method is neighbours, which are defined as two taxa that are connected by a single node in an unrooted tree Node 1 A B

  2. Distance Matrix What is required for the Neighbour joining method?

  3. First Step PAM distance 3.3 (Human - Monkey) is the minimum. So we'll join Human and Monkey to MonHum and we'll calculate the new distances. Mon-Hum Mosquito Spinach Rice Human Monkey

  4. Calculation of New Distances After we have joined two species in a subtree we have to compute the distances from every other node to the new subtree. We do this with a simple average of distances: Dist[Spinach, MonHum] = (Dist[Spinach, Monkey] + Dist[Spinach, Human])/2 = (90.8 + 86.3)/2 = 88.55 Mon-Hum Spinach Human Monkey

  5. Next Cycle Mos-(Mon-Hum) Mon-Hum Rice Spinach Mosquito Human Monkey

  6. Penultimate Cycle Mos-(Mon-Hum) Spin-Rice Mon-Hum Rice Spinach Mosquito Human Monkey

  7. Last Joining (Spin-Rice)-(Mos-(Mon-Hum)) Mos-(Mon-Hum) Spin-Rice Mon-Hum Rice Spinach Mosquito Human Monkey

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