Supporting data for the inferred ML gene tree files and MSA profiles from different datasets and models with related analyses

This repository contains the inferred ML gene tree files and MSA profiles of different concatenated MSAs, trimmed, untrimmed, or Dayhoff recoded, with different outgroup compositions, using the single-profile LG model, the best-fit single-profile model, the edge-linked proportional partitioned model, the edge-linked proportional best-fit partitioned model, the edge-unlinked partitioned model, the edge-unlinked best-fit partitioned model, the C60 and all the Strepto profile mixture models, the best-fit GTR model, as well as the simulated MSAs and the associated ML gene trees, the ML gene trees inferred from the C60 profile mixture model for the 273-rSOG, and 2026-RefSOG dataset, from the best-fit profile mixture model for the 137-rSOG dataset, all the constructed Strepto profile mixture models, and the result files from ASTRAL-pro3.