Výsledky vyhledávání - "Diego Darriba"

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

Autor: Diego Darriba, Alexandros Stamatakis, Benoit Morel, Alexey M. Kozlov, David Posada, Tomas Flouri

Publikováno v: Investigo. Repositorio Institucional de la Universidade de Vigo
Universidade de Vigo (UVigo)
RUC. Repositorio da Universidade da Coruña
instname
Molecular Biology and Evolution
Molecular biology and evolution, 37 (1), 291–294

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 orders of magnitude faster than jModelTes

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3a6e14630e6bab08f55091398e122c4

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EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences

Autor: Alexandros Stamatakis, Tomas Flouri, Alexey M. Kozlov, Benoit Morel, Pierre Barbera, Lucas Czech, Diego Darriba

Publikováno v: Systematic Biology
Systematic biology, 68 (2), 365-369

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 sequences obtained from diverse microbial e

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e616e1938567368cbae043a7dffe7a55
https://doi.org/10.1093/sysbio/syy054

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

Autor: Benoit Morel, Alexey M. Kozlov, Alexandros Stamatakis, Tomas Flouri, Diego Darriba

Publikováno v: Bioinformatics

MotivationPhylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum like-lihood (ML) criterion is known to be NP-

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7173f19b74bcc7820189a3cb5eb3ae6f
https://doi.org/10.1093/bioinformatics/btz305

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Adapting Reproducible Research Capabilities to Resilient Distributed Calculations

Autor: Diego Darriba, Antonio J. Rubio-Montero, Rafael Mayo-García, Christos Kanellopoulos, Manuel Rodríguez-Pascual, David Posada, Ognjen Prnjat

Publikováno v: International Journal of Grid and High Performance Computing. 8:58-69

Nowadays, computing calculations are becoming more and more demanding due to the huge pool of resources available. This demand must be satisfied in terms of computational efficiency and resilience, which is compromised in distributed and heterogeneou

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::b82b15d9ccd956a15545745e7c622c82
https://doi.org/10.4018/ijghpc.2016010105

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The State of Software for Evolutionary Biology

Autor: Alexandros Stamatakis, Tomas Flouri, Diego Darriba

Publikováno v: Molecular Biology and Evolution

With Next Generation Sequencing data being routinely used, evolutionary biology is transforming into a computational science. Thus, researchers have to rely on a growing number of increasingly complex software. All widely used core tools in the field

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5de948d8b079b2455bad525d43ad3f0f
https://pubmed.ncbi.nlm.nih.gov/29385525

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Resolving complex phylogeographic patterns in the Balkan Peninsula using closely related wall-lizard species as a model system

Autor: Alexey M. Kozlov, Adam D. Leaché, Alexandros Stamatakis, Aglaia Antoniou, Jelka Crnobrnja Isailovic, Nikolaos Psonis, Petros Lymberakis, Dimitris Poursanidis, Panayiota Kotsakiozi, Nikos Poulakakis, Diego Darriba, Iulian Gherghel, Oleg V. Kukushkin, Daniel Jablonski, Emmanouela Karameta

Publikováno v: Molecular Phylogenetics and Evolution

The Balkan Peninsula constitutes a biodiversity hotspot with high levels of species richness and endemism. The complex geological history of the Balkans in conjunction with the climate evolution are hypothesized as the main drivers generating this bi

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9a98dd621b27e970b101a8592af139b
https://pubmed.ncbi.nlm.nih.gov/29574273

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High-performance computing selection of models of DNA substitution for multicore clusters

Autor: Ramón Doallo, Diego Darriba, Guillermo L. Taboada, David Posada

Publikováno v: International Journal of High Performance Computing Applications
RUC. Repositorio da Universidade da Coruña
instname

[Abstract] This paper presents the high-performance computing (HPC) support of jModelTest2, the most popular bioinformatic tool for the statistical selection of models of DNA substitution. As this can demand vast computational resources, especially i

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::49444c6e0892f5c5620be705637069b5
https://doi.org/10.1177/1094342013495095

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Does the choice of nucleotide substitution models matter topologically?

Autor: Alexandros Stamatakis, Diego Darriba, Stefan Orf, Michael Hoff, Benedikt Johannes Riehm

Publikováno v: RUC. Repositorio da Universidade da Coruña
instname
BMC Bioinformatics
BMC bioinformatics, 17 (1), Art.Nr.: 143

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 203 possible nucleotide substitution mo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e7f6db8612d23599234a999d33f0652b
http://hdl.handle.net/2183/20981

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The State of Software in Evolutionary Biology

Autor: Diego Darriba, Alexandros Stamatakis, Tomas Flouri

With Next Generation Sequencing Data (NGS) coming off age and being routinely used, evolutionary biology is transforming into a data-driven science. As a consequence, researchers have to rely on a growing number of increasingly complex software. All

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9d4aa8abe303145adcbf9905abc823e3
https://doi.org/10.1101/031930

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