Figure 2 - uploaded by Joshua Stevenson
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3: 'True' splits correspond to edges in a tree which, when removed, partition the leaves of the tree. The tree is uniquely defined by this collection of splits (see Theorem 2.2.4). The leaves in the leaf-set X = {a, b, c, d, e, f } represent present-day species. The colour and position of the above splits show their correspondence with the internal edges of the tree. The edges which are directly connected to the root vertex are treated as a single edge, since both edges induce the same bipartition of taxa when removed.
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... can only know for sure that we have identified the true tree in the latter case. We aim to find the true tree by looking at each site-pattern from the alignment independently, and finding the tree which makes the most sense across all of these site-patterns (see Figure 2.1). ...
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... note that since a split is a bipartition (a partition of the leaf-set into two blocks), there is no distinction between splits A|B and B|A, and that we often consider only non-trivial splits, since trivial splits are (trivially) true. See Figure 2.3 for an example of a set of all non-trivial splits displayed by a particular 6-taxon tree. ...
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... Figure 2.1 for an example of parsimony scores for site-patterns, and Figure 2.2 for an example of the parsimony score for a split. Note that since true splits correspond to an internal edge, they have a parsimony score of 1. ...
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... Figure 2.1 for an example of parsimony scores for site-patterns, and Figure 2.2 for an example of the parsimony score for a split. Note that since true splits correspond to an internal edge, they have a parsimony score of 1. ...
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... splits each tell us something about the true phylogeny-that two subsets of species are somehow separate. In other words, they are separated by an edge in the true evolutionary tree (see Figure 2.3). Fundamentally, we can see that the core problem of phylogenetic inference is identifying these true splits. ...
