MO640 - Exercises - Phylogenetic trees: Characters and Distances, Setubal and Meidanis 1997 - chapter 6

Exercises marked with (*) require further reading/search beyond the suggested texts.

  1. For each of the input matrices below, determine whether it admits a perfect phylogeny and construct such a phylogeny if one exists.

    C1 C2 C3
    A 0 1 0
    B 0 0 1
    C 0 1 1
    D 1 1 0
    E 1 0 0
    C1 C2 C3 C4
    A 0 1 0 1
    B 0 1 1 1
    C 0 1 1 1
    D 1 1 0 0
    E 1 0 0 0

  2. For the input matrix below, determine whether it admits a perfect phylogeny and construct such a phylogeny if one exists.

    C1 C2
    A x w
    B x v
    C y w
    D z v
    E y w

  3. For the distance matrices below, construct an ultrametric matrix that falls between them, or provide an argument showing that no such matrix exists.

    A B C D E
    A 6 6.5 5 2.5
    B 1.5 4 6
    C 2.5 6.5
    D 5.5
    E
    A B C D E
    A 7.5 7 8 4
    B 3 5 8
    C 5.5 7.5
    D 8.5
    E

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© 2015 Joao Meidanis