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@@ -59,7 +59,8 @@ Key features
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*__Efficient search algorithm__: Fast and effective stochastic algorithm to reconstruct phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihood while requiring similar amount of computing time ([Nguyen et al., 2015]).
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*__Ultrafast bootstrap__: An ultrafast bootstrap approximation (UFBoot) to assess branch supports. UFBoot is 10 to 40 times faster than RAxML rapid bootstrap and obtains less biased support values ([Minh et al., 2013]; [Hoang et al., 2018]).
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*__Ultrafast model selection__: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder.
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*__Ultrafast model selection__: An ultrafast and automatic model selection (ModelFinder) which is 10 to 100 times faster than jModelTest and ProtTest. ModelFinder also finds best-fit partitioning scheme like PartitionFinder ([Kalyaanamoorthy et al., 2017]).
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*__Simulating sequences__: A fast sequence alignment simulator (AliSim) which is much more realistic than Seq-Gen and INDELible ([Ly-Trong et al., 2023]).
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*__Big Data Analysis__: Supporting huge datasets with thousands of sequences or millions of alignment sites via [checkpointing](Command-Reference#checkpointing-to-resume-stopped-run), safe numerical and low memory mode. [Multicore CPUs](Tutorial#utilizing-multi-core-cpus) and [parallel MPI system](Compilation-Guide#compiling-mpi-version) are utilized to speedup analysis.
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*__Phylogenetic testing__: Several fast branch tests like SH-aLRT and aBayes test ([Anisimova et al., 2011]) and tree topology tests like the approximately unbiased (AU) test ([Shimodaira, 2002]).
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@@ -84,11 +85,12 @@ User support
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------------
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<divclass="hline"></div>
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Please refer to the [user documentation](http://www.iqtree.org/doc/) and [frequently asked questions](http://www.iqtree.org/doc/Frequently-Asked-Questions). If you have further questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the
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Please refer to the [user documentation](http://www.iqtree.org/doc/) and
If you find a bug (e.g. when IQ-TREE prints a crash message) or want to request a new feature,
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please post an issue on GitHub: <https://github.com/iqtree/iqtree2/issues>. For other
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questions and feedback, please ask in GitHub discussions: <https://github.com/iqtree/iqtree2/discussions>
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Documentation
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IQ-TREE was funded by the [Austrian Science Fund](http://www.fwf.ac.at/) (grant no. I760-B17 from 2012-2015 and I 2508-B29 from 2016-2017), the [University of Vienna](https://www.univie.ac.at/) (Initiativkolleg I059-N from 2012-2015), the [Australian National University](https://www.anu.edu.au) (2018-onwards), [Chan-Zuckerberg Initiative](https://chanzuckerberg.com) (2020).
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[Ly-Trong et al., 2023]: https://doi.org/10.1093/bioinformatics/btad540
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[Anisimova et al., 2011]: https://doi.org/10.1093/sysbio/syr041
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[Guindon et al., 2010]: https://doi.org/10.1093/sysbio/syq010
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[Hoang et al., 2018]: https://doi.org/10.1093/molbev/msx281
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[Kalyaanamoorthy et al., 2017]: https://doi.org/10.1038/nmeth.4285
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[Minh et al., 2013]: https://doi.org/10.1093/molbev/mst024
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[Nguyen et al., 2015]: https://doi.org/10.1093/molbev/msu300
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[Schrempf et al., 2016]: https://doi.org/10.1016/j.jtbi.2016.07.042
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