ArticleBMC genomics2018
TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers.
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Who cites it
160 citing papers in PubMed.
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- A case of budding speciation in the California Floristic Province and infraspecific divergence in Abronia villosa.American journal of botany · 2026Article
- Using Nuclear Genomic Data to Address Intractable Relationships and Gene Tree Discordance in an Ancient Group of Gymnosperms (Ecology and evolution · 2026Article
- Analysis of phylogenetic signal in protein language model embeddings.Scientific reports · 2026Article
- Nuclear phylogenomic analysis of Allium (Amaryllidaceae) species from Kazakhstan reveals incomplete lineage sorting and gene flow.BMC plant biology · 2026Article
- Unraveling hidden species diversity of talpid moles using phylogenomics and skull-based deep learning.Communications biology · 2026Article
- Integrative utilization of genomic resources for improved phylogenetic resolution in Sonerileae (Melastomataceae).American journal of botany · 2026Article
- Monitoring viral evolution and epidemiological characteristics of SARS-CoV-2 during 2022-2023 using Integrated Genomic Surveillance.Communications medicine · 2026Article
- Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts.Molecular biology and evolution · 2026Article
- Chromosome-level genome assembly of the common tenrec, Tenrec ecaudatus (Schreber, 1778), a new model for early placental mammal evolution.BMC genomics · 2026Article
- The contribution of environmental DNA to exploring hypogeous fungal diversity and vulnerability.BMC microbiology · 2026Article
- Seven complete genome sequences ofMicrobiology resource announcements · 2026Article
- Origin of subgenomes in the circumboreal, allopolyploid, carnivorous plant Drosera anglica.American journal of botany · 2026Article
- Phylogenetic systematics of Juncaceae.American journal of botany · 2026Article
100 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
backgroundSequence data used in reconstructing phylogenetic trees may include various sources of error. Typically errors are detected at the sequence level, but when missed, the erroneous sequences often appear as unexpectedly long branches in the inferred phylogeny.
resultsWe propose an automatic method to detect such errors. We build a phylogeny including all the data then detect sequences that artificially inflate the tree diameter. We formulate an optimization problem, called the k-shrink problem, that seeks to find k leaves that could be removed to maximally reduce the tree diameter. We present an algorithm to find the exact solution for this problem in polynomial time. We then use several statistical tests to find outlier species that have an unexpectedly high impact on the tree diameter. These tests can use a single tree or a set of related gene trees and can also adjust to species-specific patterns of branch length. The resulting method is called TreeShrink. We test our method on six phylogenomic biological datasets and an HIV dataset and show that the method successfully detects and removes long branches. TreeShrink removes sequences more conservatively than rogue taxon removal and often reduces gene tree discordance more than rogue taxon removal once the amount of filtering is controlled.
conclusionsTreeShrink is an effective method for detecting sequences that lead to unrealistically long branch lengths in phylogenetic trees. The tool is publicly available at https://github.com/uym2/TreeShrink .
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