IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models
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This contains raw data for the manuscript “IQ2MC: A New Framework to Infer Phylogenetic Time Trees Using IQ-TREE 3 and MCMCTree with Mixture Models”
Empirical_data.zip: multiple sequence alignments for each analyzed empirical alignment, calibrated tree files, partition files, and input control files for MCMCTree.
Emprical_data_analysis.zip: scripts and MCMCTree output files for comparing divergence times under various evolutionary models and four calibration settings: young, middle, root, and all.
Simulation_data.zip: simulated DNA and AA data under six evolutionary rate categories: 1x, 2x, 4x, 6x, 8x, and 10x. DNA data use the GTR+G4 substitution model, while AA data use LG+G4 and six profile mixture models (LG+G4+C10 through LG+G4+C60).
The empirical data were derived from the following sources:
Álvarez-Carretero, Sandra, Asif U. Tamuri, Matteo Battini, Fabrícia F. Nascimento, Emily Carlisle, Robert J. Asher, Ziheng Yang, Philip C. J. Donoghue, and Mario Dos Reis. 2022. “A Species-Level Timeline of Mammal Evolution Integrating Phylogenomic Data.” Nature 602 (7896): 263–67.
Betts, Holly C., Mark N. Puttick, James W. Clark, Tom A. Williams, Philip C. J. Donoghue, and Davide Pisani. 2018. “Integrated Genomic and Fossil Evidence Illuminates Life’s Early Evolution and Eukaryote Origin.” Nature Ecology & Evolution 2 (10): 1556–62.
Morris, Jennifer L., Mark N. Puttick, James W. Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, and Philip C. J. Donoghue. 2018. “The Timescale of Early Land Plant Evolution.” Proceedings of the National Academy of Sciences of the United States of America 115 (10): E2274–83.
Reis, Mario dos, Yuttapong Thawornwattana, Konstantinos Angelis, Maximilian J. Telford, Philip C. J. Donoghue, and Ziheng Yang. 2015. “Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales.” Current Biology: CB 25 (22): 2939–50.
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Zenodo
创建时间：
2025-05-02
