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We developed a graphical interface to allow an intuitive construction of alternative family trees defined as hypotheses.
The quartet encoding strategies used in [ 14] also included calculation of the Topologically-Short Quartet (TSQ) trees, defined as follows.
The Robinson-Foulds [ 26] distance between the two trees, defined as the total number of partitions of tips implied by one tree but not the other, was 8494.
To gauge the tightness of clustering around the best tree, we computed the topological difference from the best topology for each of the 10,000 trees, defined as the number of nodes collapsed in its strict consensus with the best tree.
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The induced arrow tree (T, A ) for a tree T and a rank function rk is a complete arrow tree defined as follows.
Let be a Markov chains field defined on a Bethe tree, defined as above.
We consider (X^*) as the set of vertices of a rooted tree, defined as the right Cayley graph of the free monoid.
If {X t, t ∈ T} is a second-order Markov chain indexed by a general infinite tree with uniformly bounded tree defined as in Definition 2, we easily have f n = 1 | T ( n ) | ln P ( X - 1, X o ) + ∑ t ∈ T ( n ) { o } { - 1 } ln P ( X t | X 1 t, X 2 t ).
It is easy to see that if {X t, t ∈ T} is a S-valued Markov chains indexed by a tree defined as above, then P ( x T ( n ) ) = P ( X T ( n ) = x T ( n ) ) = p ( x o ) ∏ t ∈ T ( 1 ) n P ( x 1 x 1 t ).
As expected, juvenile Swietenia densities declined with distance from the nearest potential source tree (defined as ≥20 cm dbh) following a sigmoidal function (Fig. 3), but were not significantly associated with either percent canopy openness or PPFD (linear regression, P = 0.48 and quadratic regression P = 0.19, respectively, n = 37 plots).
A tree decomposition [117] is a mapping of a graph to a tree, defined as follows.
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