RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
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Summary
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.
- Type
- article
- Published
- 2006-10-01
- Cited by
- 15,871
- References
- 11
- Access
- Open access
- OpenAlex
- https://openalex.org/W2168696662
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:13864758
Keywords
Taxon, Inference, Computer science, Phylogenetic tree, Parallel computing
References
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- Unexpected Diversity and Complexity of the Guerrero Negro Hypersaline Microbial Mat
- Maximum likelihood of evolutionary trees: hardness and approximation
- Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion
- Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood
- A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
- RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees
- pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies
- MrBayes 3: Bayesian phylogenetic inference under mixed models
- Phylogenetic models of rate heterogeneity: a high performance computing perspective
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- Detection and quantitative assessment of horizontal gene transfer.
- Microbial ecology of a managed aquifer near the Iowa Army Ammunition Plant (Middletown, IA)
- ReXSpecies – a tool for the analysis of the evolution of gene regulation across species
- A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: Basal ecological diversification?
- Diversity and structure of ectomycorrhizal and co-associated fungal communities in a serpentine soil
- Rooting and dating maples (Acer) with an uncorrelated-rates molecular clock: implications for north American/Asian disjunctions.
- Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes
- Repeated secondary loss of adaptin complex genes in the Apicomplexa.
- Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
- A mitogenomic perspective on the phylogeny and biogeography of living caecilians (Amphibia: Gymnophiona).
- Phylogeny and mitochondrial gene order variation in Lophotrochozoa in the light of new mitogenomic data from Nemertea
- Tomato-Potato Aphid Interactions: Insights into Plant Defense and the Aphid Pest
- A multi-locus phylogeny of Nectogalini shrews and influences of the paleoclimate on speciation and evolution.
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- Evolutionary Bases of Carbohydrate Recognition and Substrate Discrimination in the ROK Protein Family
- Phylogenetic and Morphologic Analyses of a Coastal Fish Reveals a Marine Biogeographic Break of Terrestrial Origin in the Southern Caribbean
- MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies
- Phylogenetic relationships among insect orders based on three nuclear protein-coding gene sequences.
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