ArticlePeerJ2017
A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species.
Article in PeerJ, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- A scalable exemplar-based method for aligning biological taxonomies.Biodiversity data journal · 2026Article
- Pleiotropy increases with gene age in six model multicellular eukaryotes.Evolution letters · 2025Article
- Plants with higher dispersal capabilities follow 'abundant-centre' distributions but such patterns remain rare in animals.Nature communications · 2025Article
- Synthesizing decades of research into one tree for birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- A complete and dynamic tree of birds.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Is variation in female aggressiveness acrossProceedings. Biological sciences · 2025Article
- A universal tool for visualisation of networks and trees in Python.F1000Research · 2025Article
- Host habitat shapes the gut microbiomes of insular reptilian hosts in the Philippines.ISME communications · 2025Article
- PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data.BMC ecology and evolution · 2024Article
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- Genomic Assessment of the Contribution of theInternational journal of molecular sciences · 2023Article
- The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data.BMC microbiology · 2022Article
- Testing the agreement of trees with internal labels.Algorithms for molecular biology : AMB · 2021Article
- OpenTree: A Python Package for Accessing and Analyzing Data from the Open Tree of Life.Systematic biology · 2021Article
- Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life.BMC bioinformatics · 2021Article
- Untargeted In Silico Compound Classification-A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes.International journal of molecular sciences · 2021Article
- Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles.GigaScience · 2021Article
- Divergent Evolution of a Protein-Protein Interaction Revealed through Ancestral Sequence Reconstruction and Resurrection.Molecular biology and evolution · 2021Article
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Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a new supertree method that enables rapid estimation of a summary tree on the scale of millions of leaves. This supertree method summarizes a collection of input phylogenies and an input taxonomy. We introduce formal goals and criteria for such a supertree to satisfy in order to transparently and justifiably represent the input trees. In addition to producing a supertree, our method computes annotations that describe which grouping in the input trees support and conflict with each group in the supertree. We compare our supertree construction method to a previously published supertree construction method by assessing their performance on input trees used to construct the Open Tree of Life version 4, and find that our method increases the number of displayed input splits from 35,518 to 39,639 and decreases the number of conflicting input splits from 2,760 to 1,357. The new supertree method also improves on the previous supertree construction method in that it produces no unsupported branches and avoids unnecessary polytomies. This pipeline is currently used by the Open Tree of Life project to produce all of the versions of project's "synthetic tree" starting at version 5. This software pipeline is called "
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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.