Data and experiments for: "ForestPD: Maximizing Phylogenetic Diversity under Phylogenetic and Extinction Uncertainty"

Data and experiments of the paper "ForestPD: Maximizing Phylogenetic Diversity under Phylogenetic and Extinction Uncertainty" (Niels Holtgrefe, Jannik Schestag, and Norbert Zeh). All experiments use ForestPD 0.1 (https://github.com/nholtgrefe/forestpd). Files: simulations.zip: running time and peak memory of ForestPD and PDA on gene trees simulated under the multispecies coalescent (500–32,000 taxa, 100 or 1,000 trees): scripts, results and taxon costs. simulations_trees.tar.zst: the simulated gene trees (58 GB unpacked). simulations_splits.tar.zst: the split files used as PDA's input (1.4 GB unpacked). birds.zip: expected phylogenetic diversity of threatened birds over 10,000 BirdTree posterior trees with IUCN extinction probabilities, with unit costs and with annual conservation costs. tomatoes.zip: phylogenetic diversity of 13 wild tomato species over gene trees and genomic-window trees, compared with planning on the concatenated species tree. The two .tar.zst archives unpack into simulations/data/ of the unpacked simulations.zip. The birds and tomatoes experiments use published trees that must be downloaded separately. Each folder has its own README with the data, the method, how to run it, and the results files; README.md gives an overview.