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.

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Presentation transcript:

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 AB Node 1

What is required for the Neighbour joining method? Distance Matrix

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 MonkeyHumanSpinachMosquitoRice First Step

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 = ( )/2 = Mon-Hum MonkeyHumanSpinach Calculation of New Distances

HumanMosquito Mon-Hum MonkeySpinachRice Mos-(Mon-Hum) Next Cycle

HumanMosquito Mon-Hum MonkeySpinachRice Mos-(Mon-Hum) Spin-Rice Penultimate Cycle

HumanMosquito Mon-Hum MonkeySpinachRice Mos-(Mon-Hum) Spin-Rice (Spin-Rice)-(Mos-(Mon-Hum)) Last Joining