bioRxiv (Cold Spring Harbor Laboratory) · 2019 · 732 citations · 47 references
Life SciencesBioinformaticsEvolutionary BiologyGenomicsMolecular EvolutionPhylogeneticsMaximum Likelihood PhylogeneticsPhylogenetic AnalysisPhylogenetic InferencePhylogenetic Sequence AnalysisPhylogenetic Tree ReconstructionPhylogenomic AnalysisGenome-wide Phylogenetic AnalysisGenome-wide PhylogeneticsMaximum Likelihood InferenceMaximum Likelihood Tree SearchModel-based Phylogenetic InferenceNucleotide Evolution ModelsPhylogenetic Tree EstimationPhylogenetic Tree Inference
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.
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ModelFinder: fast model selection for accurate phylogenetic estimates
Subha Kalyaanamoorthy, Bùi Quang Minh, Thomas K. F. Wong et al. · Nature Methods · 2017 · 18.8K citations