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<li><ahref="doc/Estimating-amino-acid-substitution-models">QMaker</a> to estimate protein substitution matrix.</li>
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<li><ahref="doc/Command-Reference#tree-search-for-pathogen-data">CMAPLE to infer pathogen trees</a> with millions of sequences such as SARS-CoV-2.</li>
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<li><ahref="doc/Dating">IQ2MC to infer time trees</a> with MCMCtree.</li>
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<li><ahref="doc/Advanced-Tutorial#trimming-alignment-sites-by-likelihood">Trimming alignment sites</a> to improve robustness of phylogenetic analysis.</li>
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</ul>
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If you use IQ-TREE version 3 in a publication, please cite <ahref="https://doi.org/10.32942/X2P62N">Wong et al. 2025</a>.
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