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Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea.
Zhu Q, Mai U, Pfeiffer W, Janssen S, Asnicar F, Sanders JG, Belda-Ferre P, Al-Ghalith GA, Kopylova E, McDonald D, Kosciolek T, Yin JB, Huang S, Salam N, Jiao JY, Wu Z, Xu ZZ, Cantrell K, Yang Y, Sayyari E, Rabiee M, Morton JT, Podell S, Knights D, Li WJ, Huttenhower C, Segata N, Smarr L, Mirarab S, Knight R. Zhu Q, et al. Among authors: mirarab s. Nat Commun. 2019 Dec 2;10(1):5477. doi: 10.1038/s41467-019-13443-4. Nat Commun. 2019. PMID: 31792218 Free PMC article.
SEPP: SATé-enabled phylogenetic placement.
Mirarab S, Nguyen N, Warnow T. Mirarab S, et al. Pac Symp Biocomput. 2012:247-58. doi: 10.1142/9789814366496_0024. Pac Symp Biocomput. 2012. PMID: 22174280
MRL and SuperFine+MRL: new supertree methods.
Nguyen N, Mirarab S, Warnow T. Nguyen N, et al. Among authors: mirarab s. Algorithms Mol Biol. 2012 Jan 26;7(1):3. doi: 10.1186/1748-7188-7-3. Algorithms Mol Biol. 2012. PMID: 22280525 Free PMC article.
ASTRAL: genome-scale coalescent-based species tree estimation.
Mirarab S, Reaz R, Bayzid MS, Zimmermann T, Swenson MS, Warnow T. Mirarab S, et al. Bioinformatics. 2014 Sep 1;30(17):i541-8. doi: 10.1093/bioinformatics/btu462. Bioinformatics. 2014. PMID: 25161245 Free PMC article.
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