BME-like Quartet Weights for Phylogenetic Trees

Peter J. Waddell

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arXiv · 2609.00614

BME-like Quartet Weights for Phylogenetic Trees

Peter J. Waddell

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Abstract

Like pairwise distances, quartets can be highly redundant and correlated on a phylogenetic tree, and their number grows on the order of n^4 rather than n^2. I explore BME-like weights for reweighting quartet scores before summing them to score a full tree. Three weights are considered on an unrooted binary tree: w_ext(q)=2^(-I_ext(q)), w_int(q)=2^(-I_int(q)), and w_tot(q)=2^(-I_tot(q))=w_ext(q)w_int(q), where the exponents count specified internal nodes in the minimal connecting subtree of a quartet. Exact tree-shape counts, total quartet-weight sums, and internal-edge crossing sums are calculated for all unlabeled unrooted binary tree shapes on 6-10 taxa. For w_ext, the total quartet weight is tree-shape-invariant and the edge-crossing sum depends only on split size. For any n-leaf tree, we prove sum_q w_ext(q)=(n-2)(n-3)/8, and the sum over quartets crossing an internal edge with split a|b equals (a-1)(b-1)/4. Exact tree-shape-specific normalizers are also derived for w_int and w_tot. A degree-corrected hard-polytomy extension is given for multifurcating trees, and a conditional consistency result shows that these positive weights preserve consistency when the underlying quartet estimates are themselves consistent for the true induced quartet states. These results provide a mathematical foundation for evaluating and applying BME-like quartet weights to reduce redundancy with the particular aim of improving statistical efficiency with finite data.

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Peter J. Waddell. 2026-09-01. BME-like Quartet Weights for Phylogenetic Trees. https://arxiv.org/abs/2609.00614

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