Diego Darriba
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View article: ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models
ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models Open
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 tha…
View article: RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference Open
Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree under the popular maximum likelihood (ML) criterion is known…
View article: ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models
ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models Open
ModelTest-NG is a re-implementation 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 th…
View article: RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference Open
Motivation Phylogenies 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 kno…
View article: EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences Open
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 …
View article: EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences
EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences Open
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 …
View article: The State of Software for Evolutionary Biology
The State of Software for Evolutionary Biology Open
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 i…
View article: Does the choice of nucleotide substitution models matter topologically?
Does the choice of nucleotide substitution models matter topologically? Open
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 subs…
View article: Prediction of missing sequences and branch lengths in phylogenomic data
Prediction of missing sequences and branch lengths in phylogenomic data Open
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 sequences is that the …
View article: The State of Software in Evolutionary Biology
The State of Software in Evolutionary Biology Open
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 sof…
View article: The impact of partitioning on phylogenomic accuracy
The impact of partitioning on phylogenomic accuracy Open
Several strategies have been proposed to assign substitution models in phylogenomic datasets, or partitioning. The accuracy of these methods, and most importantly, their impact on phylogenetic estimation has not been thoroughly assessed us…
View article: PartitionTest test suite empirical additional
PartitionTest test suite empirical additional Open
PartitionTest test suite
View article: PartitionTest test suite test empirical additional files
PartitionTest test suite test empirical additional files Open
PartitionTest test suite
View article: PartitionTest test suite mosaic additional
PartitionTest test suite mosaic additional Open
PartitionTest test suite
View article: PartitionTest test suite multigene additional
PartitionTest test suite multigene additional Open
PartitionTest test suite
View article: PartitionTest test suite ratevar additional
PartitionTest test suite ratevar additional Open
PartitionTest test suite