Darriba, D. | Search bioRxiv

bioRxiv2019

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

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 than jModelTest and ProtTest but equally accurate, and introduces several new features, such as ascertainment bias correction, mixture and FreeRate models, or the automatic processing of partitioned datasets. ModelTest-NG is available under a GNU GPL3 license at https://github.com/ddarriba/modeltest.

bioinformatics↗

bioRxiv2018

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

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-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.\n\nResultsWe present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML- NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.\n\nAvailabilityThe code is available under GNU GPL at https://github.com/amkozlov/raxml-ng.RAxML-NG web service (maintained by Vital- IT) is available at https://raxml-ng.vital-it.ch/.\n\nContactalexey.kozlov@h-its.org

bioinformatics↗