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Not all branches are equal: Branch Length Evaluation for Phylogenetic Diversity analysis.

Miranda-Esquivel, D. R.

2025-01-14 evolutionary biology
10.1101/2025.01.11.632535 bioRxiv
Show abstract

Phylogenetic Diversity (PD) is a crucial metric in evolutionary and conservation studies; however, its dependence on branch-length information can be a source of uncertainty. Branch Length Evaluation for Phylogenetic Diversity analysis (BLEPD) is a free and open-source R program used to quantify the uncertainty in PD calculations caused by varying branch length information. It offers two main approaches: resampling branch lengths within the phylogenetic tree, and modifying individual branch lengths. By comparing the initial and selected areas after resampling or modification, BLEPD allows researchers to assess the sensitivity of PD to these variations. This analysis of branch length sensitivity provides valuable insights into the robustness of PD results and their dependence on this information. BLEPD may improve the interpretation of PD analyses in evolutionary, conservation, and ecological studies.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.