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smirarab authored May 17, 2018
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- All the versions between 4.7.4 and 5.1.0 corresponds to ASTRAL-II, described in:
* Mirarab, Siavash, and Tandy Warnow. “ASTRAL-II: Coalescent-Based Species Tree Estimation with Many Hundreds of Taxa and Thousands of Genes.”. Bioinformatics (ISMB special issue) 31 (12): i44–i52. 2015. [doi:10.1093/bioinformatics/btv234](http://bioinformatics.oxfordjournals.org/content/31/12/i44)
- Since version 5.1.1, the code corresponds to ASTRAL-III, described in:
* Zhang, Chao, Erfan Sayyari, and Siavash Mirarab. “ASTRAL-III: Increased Scalability and Impacts of Contracting Low Support Branches.” In Comparative Genomics: 15th International Workshop, RECOMB CG, 2017. [doi:10.1007/978-3-319-67979-2_4](https://doi.org/10.1007/978-3-319-67979-2_4).
* Zhang, Chao, Maryam Rabiee, Erfan Sayyari, and Siavash Mirarab. “ASTRAL-III: Polynomial Time Species Tree Reconstruction from Partially Resolved Gene Trees.” BMC Bioinformatics 19, no. S6 (May 8, 2018): 153. https://doi.org/10.1186/s12859-018-2129-y.
- Since version 4.10.0, ASTRAL can also compute branch length (in coalescent units) and a measure of support called “local posterior probability”, described here:
* Sayyari, Erfan, and Siavash Mirarab. “Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies.” Molecular Biology and Evolution 33 (7): 1654–68. 2016. [doi:10.1093/molbev/msw079](http://mbe.oxfordjournals.org/content/early/2016/05/12/molbev.msw079.short?rss=1)

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