ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy,Subha Kalyaanamoorthy,Bui Quang Minh,Thomas K. F. Wong,Thomas K. F. Wong,Arndt von Haeseler,Arndt von Haeseler,Lars S. Jermiin,Lars S. Jermiin +8 more
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TLDR
ModelFinder is presented, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.Abstract:
Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates by incorporating a model of rate heterogeneity across sites not previously considered in this context and by allowing concurrent searches of model space and tree space.read more
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IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era.
Bui Quang Minh,Heiko A. Schmidt,Olga Chernomor,Dominik Schrempf,Dominik Schrempf,Michael D. Woodhams,Arndt von Haeseler,Arndt von Haeseler,Robert Lanfear +8 more
TL;DR: Some notable features of IQ-TREE version 2 are described and the key advantages over other software are highlighted.
Journal ArticleDOI
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Jaime Huerta-Cepas,Damian Szklarczyk,Davide Heller,Ana Hernández-Plaza,Sofia K. Forslund,Helen Cook,Daniel R. Mende,Ivica Letunic,Thomas Rattei,Lars Juhl Jensen,Christian von Mering,Peer Bork +11 more
TL;DR: eggNOG as discussed by the authors is a public database of orthology relationships, gene evolutionary histories and functional annotations, with a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes.
Journal ArticleDOI
RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.
Alexey M. Kozlov,Diego Darriba,Tomas Flouri,Benoit Morel,Alexandros Stamatakis,Alexandros Stamatakis +5 more
TL;DR: RAxML-NG is presented, a from-scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML, which offers improved accuracy, flexibility, speed, scalability, and usability compared with RAx ML/ exaML.
Journal ArticleDOI
Asymmetric paralog evolution between the “cryptic” gene Bmp16 and its well-studied sister genes Bmp2 and Bmp4
TL;DR: The phylogenetic analysis complemented with synteny analyses suggests that Bmp2, -4 and -16 are remnants of a gene quartet that originated during the two rounds of whole-genome duplication (2R-WGD) early in vertebrate evolution.
Journal ArticleDOI
PhyloSuite: an integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
TL;DR: PhyloSuite is designed for both beginners and experienced researchers, allowing the former to quick‐start their way into phylogenetic analysis, and the latter to conduct, store and manage their work in a streamlined way, and spend more time investigating scientific questions instead of wasting it on transferring files from one software program to another.
References
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Journal ArticleDOI
MODELTEST: testing the model of DNA substitution.
David Posada,Keith A. Crandall +1 more
TL;DR: The program MODELTEST uses log likelihood scores to establish the model of DNA evolution that best fits the data.
Journal ArticleDOI
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
Stéphane Guindon,Jean-François Dufayard,Vincent Lefort,Maria Anisimova,Wim Hordijk,Olivier Gascuel +5 more
TL;DR: A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
Journal ArticleDOI
IQ-TREE: A fast and effective stochastic algorithm for estimating maximum likelihood phylogenies
TL;DR: It is shown that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented and found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space.
Journal ArticleDOI
jModelTest 2: more models, new heuristics and parallel computing.
TL;DR: jModelTest 2: more models, new heuristics and parallel computing Diego Darriba, Guillermo L. Taboada, Ramón Doallo and David Posada.
Journal ArticleDOI
jModelTest: Phylogenetic Model Averaging
TL;DR: jModelTest is a new program for the statistical selection of models of nucleotide substitution based on "Phyml" that implements 5 different selection strategies, including "hierarchical and dynamical likelihood ratio tests," the "Akaike information criterion", the "Bayesian information criterion," and a "decision-theoretic performance-based" approach.
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