Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
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Summary
Two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models are described and implemented in an open-source program, PartitionFinder, which it is hoped will encourage the objective selection of partitions and thus lead to improvements in phylogenetic analyses.
- Type
- article
- Published
- 2012-06-01
- Cited by
- 5,502
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W2133870991
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:14773390
Keywords
Phylogenetic tree, Akaike information criterion, Selection (genetic algorithm), Biology, Substitution (logic)
References
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- Bayesian phylogenetic analysis of combined data.
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- New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
- Recent trends in molecular phylogenetic analysis: where to next?
- jModelTest: phylogenetic model averaging.
- A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera:Papilionidae).
- Phylogenetic mixture models for proteins
- The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics.
- Phylogenetic systematics and biogeography of hummingbirds: Bayesian and maximum likelihood analyses of partitioned data and selection of an appropriate partitioning strategy.
- Out of the Andes: patterns of diversification in clearwing butterflies
- Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation.
Cited by
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- Domestication and the Mitochondrial Genome: Comparing Patterns and Rates of Molecular Evolution in Domesticated Mammals and Birds and Their Wild Relatives
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- Genomic support for a moa-tinamou clade and adaptive morphological convergence in flightless ratites.
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- Ophiocordyceps myrmicarum, a new species infecting invasive Myrmica rubra in Maine.
- Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences
- Species on the rocks: Systematics and biogeography of the rock-dwelling Ptyodactylus geckos (Squamata: Phyllodactylidae) in North Africa and Arabia.
- Species-Level Phylogeny and Polyploid Relationships in Hordeum (Poaceae) Inferred by Next-Generation Sequencing and In Silico Cloning of Multiple Nuclear Loci
- The biogeographic origin of a radiation of trees in Madagascar: implications for the assembly of a tropical forest biome
- Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)
- Trends in substitution models of molecular evolution
- Species discovery and validation in a cryptic radiation of endangered primates: coalescent‐based species delimitation in Madagascar's mouse lemurs
- Oceanic dispersal, vicariance and human introduction shaped the modern distribution of the termites Reticulitermes, Heterotermes and Coptotermes
- Application of multigene phylogenetics and site‐stripping to resolve intraordinal relationships in the Rhodymeniales (Rhodophyta)
- Phylogeny of the titi monkeys of the Callicebus moloch group (Pitheciidae, Primates)
- A cryptic palm-pitviper species (Squamata: Viperidae: Bothriechis) from the Costa Rican highlands, with notes on the variation within B. nigroviridis.
- Molecular phylogeny of the aquatic beetle family Noteridae (Coleoptera: Adephaga) with an emphasis on data partitioning strategies.
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