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    NNI (Nearest Neighbour Interchange)


    Searches for a better (more parsimonious) tree by swapping the relative positions of subtrees separated by one edge. At each inner edge (i.e. at non-leaf edges) three different topologies are possible.

    Testing these 3 possible topologies and keeping the best of them, is called "Nearest Neighborhood Interchange" (NNI).


    Possible topologies tested by NNI  

    The 3 different topologies checked by performing a NNI are

    (A,B,C = subtrees; R = rest of tree)

    R           R           R
     \           \           \
     /\          /\          /\
    A  \        B  \        C  \
       /\          /\          /\
      B  C        A  C        B  A

    Note: there are no other possible topologies containing A,B,C and R!






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