ArticlePeerJ2016
PhySortR: a fast, flexible tool for sorting phylogenetic trees in R.
Article in PeerJ, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- ImprovedMicroorganisms · 2022Article
- The evolution of huge Y chromosomes inPhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Article
- Multiple waves of viral invasions in Symbiodiniaceae algal genomes.Virus evolution · 2022Article
- Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery.Molecular biology and evolution · 2021Article
- Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis.Molecular biology and evolution · 2021Article
- Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Genome Analyses of the Microalga Picochlorum Provide Insights into the Evolution of Thermotolerance in the Green Lineage.Genome biology and evolution · 2018Article
- Plastid and mitochondrial genomes of Coccophora langsdorfii (Fucales, Phaeophyceae) and the utility of molecular markers.PloS one · 2017Article
- Article
- SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees.PeerJ · 2016Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A frequent bottleneck in interpreting phylogenomic output is the need to screen often thousands of trees for features of interest, particularly robust clades of specific taxa, as evidence of monophyletic relationship and/or reticulated evolution. Here we present PhySortR, a fast, flexible R package for classifying phylogenetic trees. Unlike existing utilities, PhySortR allows for identification of both exclusive and non-exclusive clades uniting the target taxa based on tip labels (i.e., leaves) on a tree, with customisable options to assess clades within the context of the whole tree. Using simulated and empirical datasets, we demonstrate the potential and scalability of PhySortR in analysis of thousands of phylogenetic trees without a priori assumption of tree-rooting, and in yielding readily interpretable trees that unambiguously satisfy the query. PhySortR is a command-line tool that is freely available and easily automatable.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.