Dataset for Two Step Species Tree Inference under the Multispecies Coalescent Using Full-Likelihood

This dataset contains simulation and inference scripts used for Two Step Species Tree Inference under the Multispecies Coalescent Using Full-Likelihood. The simulation part includes scripts for generating gene trees under the MSC model with varying levels of incomplete lineage sorting, followed by DNA sequence simulation under the Jukes-Cantor (JC) substitution model. The inference parts provides analysis scripts for five coalescent-based species tree estimation methods: ASTRAL (quartet-based summary method), MT (Maximum Tree), MP-EST (triplet-based pseudo-likelihood), RevBayes-MSC (two-step full-likelihood using point estimates), and RevBayes-IS (two-step full-likelihood using importance sampling with posterior gene tree samples).