MO640 - Exercises - SCJ Distances and Medians, Feijao and Meidanis 2011

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

3. Considering again the data from Exercise 1, can you find a more parsimonious topology than the one shown, for these 5 genomes, under the SCJ distance?

five genomes phylogeny

Answer:

The topology in the figure below gives a better total branch length.

With ancestral genomes computed by the weighted median method, as shown in the figure, we get a total branch length (TBL) of 5, which is less that the minimum TBL of the topology shown in Exercise 1.

To compute this total branch length, notice that, in the figure, we have the branch lengths of the edges leading to leaves. For the edges linking internal nodes, observe that their lengths are zero, except for the edge A1-A2, whose length is 2. Adding all the lengths we get 5.

most parsimonious phylogeny


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