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Jacob L. Steenwyk, Thomas J. Buida, III, Yuanning Li, Xing-Xing Shen, and Antonis Rokas. Clipkit: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biology, 18(12):1–17, 12 2020. URL: https://doi.org/10.1371/journal.pbio.3001007, doi:10.1371/journal.pbio.3001007.
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Chao Zhang, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. Astral-iii: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics, 19(6):153, 2018. URL: https://doi.org/10.1186/s12859-018-2129-y, doi:10.1186/s12859-018-2129-y.