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Advances in Applied Mathematics
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Advances in Applied Mathematics
Article . 2013
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Advances in Applied Mathematics
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Polyhedral combinatorics of UPGMA cones

Authors: Ruth Davidson; Seth Sullivant;

Polyhedral combinatorics of UPGMA cones

Abstract

Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive orthant induced by classifying the input vectors according to tree topologies returned by the algorithm. The partition lattice informs the study of UPGMA trees. We give a closed form for the extreme rays of UPGMA cones on n taxa, and compute the normalized volumes of the UPGMA cones for small n. Keywords: phylogenetic trees, polyhedral combinatorics, partition lattice

Keywords

Applied Mathematics, Populations and Evolution (q-bio.PE), Polyhedral combinatorics, Quantitative Biology - Quantitative Methods, 92D15, 52B05, 90C57, 05C07, 06A07, Phylogenetic trees, FOS: Biological sciences, FOS: Mathematics, Mathematics - Combinatorics, Partition lattice, Combinatorics (math.CO), Quantitative Biology - Populations and Evolution, Quantitative Methods (q-bio.QM)

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
5
Average
Average
Average
Green
hybrid