Simulated species trees and gene trees for two sweeps used to benchmark species-tree inference Every size has 5 replicates (R1–R5), each a species tree (stree.trees) and its gene trees (allgt.tre, one Newick tree per line). The data were generated by the benchmark harness phylo-bench (commit 7aa3c87e49bfa6b6032ff81759b21740327385fb), unchanged, with the simphy-x engine in compat mode, which produces trees byte-identical to SimPhy 1.0.2. For every size T taxa × G genes: which runs (see provenance/simphy-commands.txt for each data set's recorded command line): then concatenates each replicate's gene trees into allgt.tre (dropping SimPhy's 00 label suffixes) with the harness's…
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Ashrafur Rahman
risenfromashes
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