ArticleBMC genomics2020
A generalized Robinson-Foulds distance for labeled trees.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
15 citing papers in PubMed, 35 citations in OpenAlex.
- CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.Microbial genomics · 2026Article
- Bacterial genome reconstruction and community profiling in Neotropical Drosophila.Scientific reports · 2026Article
- Assessing the impact of phylogenetic reconstruction error on genetic reassortment inference in segmented viruses.PloS one · 2026Article
- Evaluating Pretrained Protein Language Model Embeddings as Proxies for Functional Similarity.Journal of molecular evolution · 2025Article
- The path-label reconciliation (PLR) dissimilarity measure for gene trees.Algorithms for molecular biology : AMB · 2025Article
- Systematic analysis of some Astereae (Asteraceae) species by Integrating pollen morphology and molecular evidence.Frontiers in plant science · 2025Article
- Oncotree2vec - a method for embedding and clustering of tumor mutation trees.Bioinformatics (Oxford, England) · 2024Article
- TheJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- AGO, a Framework for the Reconstruction of Ancestral Syntenies and Gene Orders.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters.bioRxiv : the preprint server for biology · 2023Article
- The evolution of morphological development is congruent with the species phylogeny in the genusFrontiers in microbiology · 2023Article
- Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- A Linear Time Solution to the Labeled Robinson-Foulds Distance Problem.Systematic biology · 2022Article
- The Generalized Robinson-Foulds Distance for Phylogenetic Trees.Journal of computational biology : a journal of computational molecular cell biology · 2021Article
- The Bourque distances for mutation trees of cancers.Algorithms for molecular biology : AMB · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Robinson-Foulds (RF) distance is a well-established measure between phylogenetic trees. Despite a lack of biological justification, it has the advantages of being a proper metric and being computable in linear time. For phylogenetic applications involving genes, however, a crucial aspect of the trees ignored by the RF metric is the type of the branching event (e.g. speciation, duplication, transfer, etc).
resultsWe extend RF to trees with labeled internal nodes by including a node flip operation, alongside edge contractions and extensions. We explore properties of this extended RF distance in the case of a binary labeling. In particular, we show that contrary to the unlabeled case, an optimal edit path may require contracting "good" edges, i.e. edges shared between the two trees.
conclusionsWe provide a 2-approximation algorithm which is shown to perform well empirically. Looking ahead, computing distances between labeled trees opens up a variety of new algorithmic directions.Implementation and simulations available at https://github.com/DessimozLab/pylabeledrf .
Indexed as
Identifiers
What OpenQuestion holds
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.