FastTree 2--approximately maximum-likelihood trees for large alignments.
Reads0
Chats0
TLDR
Improvements to FastTree are described that improve its accuracy without sacrificing scalability, and FastTree 2 allows the inference of maximum-likelihood phylogenies for huge alignments.Abstract:
Background
We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacrificing scalability.read more
Citations
More filters
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
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
Pfam: the protein families database.
Robert D. Finn,Alex Bateman,Jody Clements,Penelope Coggill,Ruth Y. Eberhardt,Sean R. Eddy,Andreas Heger,Kirstie Hetherington,Liisa Holm,Jaina Mistry,Erik L. L. Sonnhammer,John Tate,Marco Punta +12 more
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Journal ArticleDOI
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
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
Daniel McDonald,Morgan N. Price,Julia K. Goodrich,Julia K. Goodrich,Eric P. Nawrocki,Todd Z. DeSantis,Alexander J. Probst,Alexander J. Probst,Gary L. Andersen,Rob Knight,Rob Knight,Philip Hugenholtz +11 more
TL;DR: A ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology is developed and used to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences.
References
More filters
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Journal ArticleDOI
Confidence limits on phylogenies: an approach using the bootstrap.
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Journal ArticleDOI
Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach.
TL;DR: A nonparametric approach to the analysis of areas under correlated ROC curves is presented, by using the theory on generalized U-statistics to generate an estimated covariance matrix.
Journal ArticleDOI
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
Journal ArticleDOI
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
Related Papers (5)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh,Daron M. Standley +1 more
QIIME allows analysis of high-throughput community sequencing data.
J. Gregory Caporaso,Justin Kuczynski,Jesse Stombaugh,Kyle Bittinger,Frederic D. Bushman,Elizabeth K. Costello,Noah Fierer,Antonio Gonzalez Peña,Julia K. Goodrich,Jeffrey I. Gordon,Gavin A. Huttley,Scott T. Kelley,Dan Knights,Jeremy E. Koenig,Ruth E. Ley,Catherine A. Lozupone,Daniel McDonald,Brian D. Muegge,Meg Pirrung,Jens Reeder,Joel Sevinsky,Peter J. Turnbaugh,William A. Walters,Jeremy Widmann,Tanya Yatsunenko,Jesse R. Zaneveld,Rob Knight,Rob Knight +27 more