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jModelTest 2: more models, new heuristics and parallel computing.
Darriba D, Taboada GL, Doallo R, Posada D. Darriba D, et al. Nat Methods. 2012 Jul 30;9(8):772. doi: 10.1038/nmeth.2109. Nat Methods. 2012. PMID: 22847109 Free PMC article. No abstract available. selection of nucleotide substitution models on the cloud.
Santorum JM, Darriba D, Taboada GL, Posada D. Santorum JM, et al. Among authors: darriba d. Bioinformatics. 2014 May 1;30(9):1310-1. doi: 10.1093/bioinformatics/btu032. Epub 2014 Jan 21. Bioinformatics. 2014. PMID: 24451621 Free PMC article.
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences.
Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A. Barbera P, et al. Among authors: darriba d. Syst Biol. 2019 Mar 1;68(2):365-369. doi: 10.1093/sysbio/syy054. Syst Biol. 2019. PMID: 30165689 Free PMC article.
Prediction of missing sequences and branch lengths in phylogenomic data.
Darriba D, Weiß M, Stamatakis A. Darriba D, et al. Bioinformatics. 2016 May 1;32(9):1331-7. doi: 10.1093/bioinformatics/btv768. Epub 2016 Jan 5. Bioinformatics. 2016. PMID: 26733454
ProtTest 3: fast selection of best-fit models of protein evolution.
Darriba D, Taboada GL, Doallo R, Posada D. Darriba D, et al. Bioinformatics. 2011 Apr 15;27(8):1164-5. doi: 10.1093/bioinformatics/btr088. Epub 2011 Feb 17. Bioinformatics. 2011. PMID: 21335321 Free PMC article.
The phylogenetic likelihood library.
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A. Flouri T, et al. Among authors: darriba d. Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30. Syst Biol. 2015. PMID: 25358969 Free PMC article.
The State of Software for Evolutionary Biology.
Darriba D, Flouri T, Stamatakis A. Darriba D, et al. Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014. Mol Biol Evol. 2018. PMID: 29385525 Free PMC article. Review.
Does the choice of nucleotide substitution models matter topologically?
Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A. Hoff M, et al. Among authors: darriba d. BMC Bioinformatics. 2016 Mar 24;17:143. doi: 10.1186/s12859-016-0985-x. BMC Bioinformatics. 2016. PMID: 27009141 Free PMC article.
Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system.
Psonis N, Antoniou A, Karameta E, Leaché AD, Kotsakiozi P, Darriba D, Kozlov A, Stamatakis A, Poursanidis D, Kukushkin O, Jablonski D, Crnobrnja-Isailović J, Gherghel I, Lymberakis P, Poulakakis N. Psonis N, et al. Among authors: darriba d. Mol Phylogenet Evol. 2018 Aug;125:100-115. doi: 10.1016/j.ympev.2018.03.021. Epub 2018 Mar 21. Mol Phylogenet Evol. 2018. PMID: 29574273
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. Kozlov AM, et al. Among authors: darriba d. Bioinformatics. 2019 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305. Bioinformatics. 2019. PMID: 31070718 Free PMC article.
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