PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

By Robert Lanfear, P. Frandsen, A. Wright, Tereza Senfeld, B. Calcott. Molecular biology and evolution, 2016

5,145 citations recorded by the source corpus.

Subfields: Ecology, Evolution, Behavior and Systematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/be937d4db2fb29842e427badd4d3ca77c463077a

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Citations in the corpus

Using PhyloSuite for molecular phylogeny and tree‐based analyses (2023, background): “In multilocus datasets, different loci (gene or codon sites) may evolve at different rates and patterns, as they often have different biological functions and evolve under different selection pressures [37, 38].”
PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies (2019, methodology): “…evolutionary model and/ or partitioning scheme using modelfinder (Kalyaanamoorthy, Minh, Wong, von Haeseler, & Jermiin, 2017) or P artition f inder (Lanfear, Frandsen, Wright, Senfeld, & Calcott, 2017); (vii) batch‐phylogeny reconstruction using iq ‐ tree (maximum likelihood) (Nguyen, Schmidt, von…”
Owlflies are derived antlions: anchored phylogenomics supports a new phylogeny and classification of Myrmeleontidae (Neuroptera) (2018, methodology): “The partitioning scheme and best-fitting substitution model for each partition were selected using Bayesian Information Criterion in PartitionFinder2 (Lanfear et al., 2016).”
Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera) (2018, methodology): “For the supermatrix approach, the concatenated amino acid and nucleotide alignments were initially partitioned by loci, and these partitions were then combined into metapartitions with PartitionFinder 2 (Lanfear et al., 2016) using the rcluster search algorithm (Lanfear et al.”
Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits (2018, positive): “For all ML analyses, we first performed 20 independent runs using random starting trees under the best-fit model (preliminary analyses) or the modeling scheme predicted by PartitionFinder2 and from these, chose the best scoring tree.”
IQ-TREE 3: phylogenomic inference software using complex evolutionary models (2026, neutral): “Partitioned models are available in RAxML (Stamatakis 2014), RAxML-NG (Kozlov et al. 2019), and IQ-TREE 2 (Minh et al. 2020b); and tools like PartitionFinder (Lanfear et al. 2017) can merge partitions to reduce over-parameterization.”
Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming (2020, methodology): “The best‐fit model of the whole plastome for the ML analysis was TVM+ I+ G, and for BI analysis, it was GTR+ Г+ I, as estimated by PartitionFinder (Lanfear et al., 2016).”
Higher‐level phylogeny of longhorn beetles (Coleoptera: Chrysomeloidea) inferred from mitochondrial genomes (2020, methodology): “Based on the tests of phylogenetic tree building parameters in Nie et al. (2020) and the heterogeneity of sequence divergence of PCGs, the PCGs data were chosen for the phylogenetic analyses as follows: (i) 13 mitochondrial PCGs (13PCGs) partitioned by gene and by codon using PartitionFinder2 (Lanfe”