Listar por autor "Stamatakis, Alexandros"
Mostrando ítems 1-6 de 6
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Does the choice of nucleotide substitution models matter topologically?
Hoff, Michael; Orf, Stefan; Riehm, Benedikt; Darriba, Diego; Stamatakis, Alexandros (BioMed Central Ltd., 2016-03-24)[Abstract] Background: In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all ... -
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
Barbera, Pierre; Kozlov, Alexey M.; Czech, Lucas; Morel, Benoit; Darriba, Diego; Flouri, Tomas; Stamatakis, Alexandros (Oxford University Press, 2019-03-01)[Abstract]: Next generation sequencing (NGS) technologies have led to a ubiquity of molecular sequence data. This data avalanche is particularly challenging in metagenetics, which focuses on taxonomic identification of ... -
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
Darriba, Diego; Posada, David; Kozlov, Alexey M.; Stamatakis, Alexandros; Morel, Benoit; Flouri, Tomas (Oxford University Press, 2019-08-21)[Abstract] ModelTest-NG is a reimplementation from scratch of jModelTest and ProtTest, two popular tools for selecting the best-fit nucleotide and amino acid substitution models, respectively. ModelTest-NG is one to two ... -
Prediction of missing sequences and branch lengths in phylogenomic data
Darriba, Diego; Weiß, Michael; Stamatakis, Alexandros (Oxford University Press, 2016-01-05)[Abstract] Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition ... -
The Phylogenetic Likelihood Library
Flouri, Tomas; Izquierdo-Carrasco, F.; Darriba, Diego; Aberer, Andre J.; Nguyen, Lam-Tung; Minh, B.Q.; Haeseler, Arndt von; Stamatakis, Alexandros (Oxford University Press, 2015-03-01)[Abstract] We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized application programming interface for developing likelihood-based phylogenetic inference and postanalysis software. The PLL implements ... -
The Wall Lizards of the Balkan Peninsula: Tackling Questions at the Interphase of Phylogenomics and Population Genomics
Psonis, Nikolaos; Antioniou, Aglaia; Karameta, Emmanouela; Darriba, Diego; Stamatakis, Alexandros; Lymberakis, Petros; Poulakakis, Nikos (Elsevier, 2021)[Abstract] Wall lizards of the genus Podarcis (Sauria, Lacertidae) are the predominant reptile group in southern Europe, including 24 recognized species. Mitochondrial DNA data have shown that, with the exception of P. ...