IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era
Preprint
- 21 November 2019
- preprint
- Published by Cold Spring Harbor Laboratory in bioRxiv
- p. 849372
- https://doi.org/10.1101/849372
Abstract
IQ-TREE (http://www.iqtree.org) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.Keywords
All Related Versions
- Published version: Molecular Biology and Evolution, 37 (5), 1530.
This publication has 44 references indexed in Scilit:
- Ultrafast Approximation for Phylogenetic BootstrapMolecular Biology and Evolution, 2013
- A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic LissamphibiaPLOS ONE, 2012
- PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic AnalysesMolecular Biology and Evolution, 2012
- Survey of Branch Support Methods Demonstrates Accuracy, Power, and Robustness of Fast Likelihood-based Approximation SchemesSystematic Biology, 2011
- New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0Systematic Biology, 2010
- FastTree 2 – Approximately Maximum-Likelihood Trees for Large AlignmentsPLOS ONE, 2010
- Accounting for Solvent Accessibility and Secondary Structure in Protein Phylogenetics Is Clearly BeneficialSystematic Biology, 2010
- Inferring confidence sets of possibly misspecified gene treesProceedings Of The Royal Society B-Biological Sciences, 2002
- Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic InferenceMolecular Biology and Evolution, 1999
- Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 1981