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We call the vectors v T the balanced minimum evolution vectors (or BME vectors).
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The following facts follow from the definition of the balanced minimum evolution tree: The vertices of the BME polytope are the BME vectors of binary trees.
This result provides a weighted least squares rationale for the minimization of (2), and highlights the importance of understanding the balanced minimum evolution polytope: The balanced minimum evolution polytope is the convex hull of the vectors { [ λ 12 T, λ 13 T,..., λ i j T,..., λ n − 1, n T ] : T i s a t r e e w i t h n l e a v e s } Example.
Further, for the construction of phylogenetic trees, the principle of minimum evolution has been considered.
The alternative methods of phylogenetic tree construction, minimum evolution and maximum likelihood, were tested, but the support for the minimum evolution tree was not sufficient (data not shown).
The phylogenetic tree was produced by the minimum evolution method and 1000 bootstrap iteration.
Four methods were employed, Neighbor-joining (NJ), UPGMA, Maximum parsimony, and Minimum evolution.
The minimum evolution criterion was used and branch lengths were allowed to be negative except when calculating tree scores.
A Minimum Evolution tree was generated by the Neighbor-Joining method with level 1 Close-Neighbor-Interchange.
The Minimum evolution algorithm was applied based on the Nucleotide Maximum Composite Likelihood analysis of all positions.
Phylogenetic analyses with Poisson Model, including NJ, minimum evolution, and bootstrap analyses with 1000 replicates, were performed using MEGA 4.0 [4.0.
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