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Items: 11

1.

ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models.

Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B, Flouri T.

Mol Biol Evol. 2019 Aug 20. pii: msz189. doi: 10.1093/molbev/msz189. [Epub ahead of print]

PMID:
31432070
2.

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.

Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A.

Bioinformatics. 2019 Nov 1;35(21):4453-4455. doi: 10.1093/bioinformatics/btz305.

3.

EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences.

Barbera P, Kozlov AM, Czech L, Morel B, Darriba D, Flouri T, Stamatakis A.

Syst Biol. 2019 Mar 1;68(2):365-369. doi: 10.1093/sysbio/syy054.

4.

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.

Mol Phylogenet Evol. 2018 Aug;125:100-115. doi: 10.1016/j.ympev.2018.03.021. Epub 2018 Mar 21.

PMID:
29574273
5.

The State of Software for Evolutionary Biology.

Darriba D, Flouri T, Stamatakis A.

Mol Biol Evol. 2018 May 1;35(5):1037-1046. doi: 10.1093/molbev/msy014. Review.

6.

Does the choice of nucleotide substitution models matter topologically?

Hoff M, Orf S, Riehm B, Darriba D, Stamatakis A.

BMC Bioinformatics. 2016 Mar 24;17:143. doi: 10.1186/s12859-016-0985-x.

7.

Prediction of missing sequences and branch lengths in phylogenomic data.

Darriba D, Weiß M, Stamatakis A.

Bioinformatics. 2016 May 1;32(9):1331-7. doi: 10.1093/bioinformatics/btv768. Epub 2016 Jan 5.

PMID:
26733454
8.

The phylogenetic likelihood library.

Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.

Syst Biol. 2015 Mar;64(2):356-62. doi: 10.1093/sysbio/syu084. Epub 2014 Oct 30.

9.

jmodeltest.org: selection of nucleotide substitution models on the cloud.

Santorum JM, Darriba D, Taboada GL, Posada D.

Bioinformatics. 2014 May 1;30(9):1310-1. doi: 10.1093/bioinformatics/btu032. Epub 2014 Jan 21.

10.

jModelTest 2: more models, new heuristics and parallel computing.

Darriba D, Taboada GL, Doallo R, Posada D.

Nat Methods. 2012 Jul 30;9(8):772. doi: 10.1038/nmeth.2109. No abstract available.

11.

ProtTest 3: fast selection of best-fit models of protein evolution.

Darriba D, Taboada GL, Doallo R, Posada D.

Bioinformatics. 2011 Apr 15;27(8):1164-5. doi: 10.1093/bioinformatics/btr088. Epub 2011 Feb 17.

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