ArticleBMC genomics2015
ASTRID: Accurate Species TRees from Internode Distances.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 76 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
76 citing papers in PubMed.
- Triplet-based species tree estimation: Sensitivity to gene tree rooting (or lack thereof).PLoS computational biology · 2026Article
- Species Tree Branch Length Estimation despite Incomplete Lineage Sorting, Duplication, and Loss.Genome biology and evolution · 2025Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii.Nature communications · 2025Article
- Integrating phylogenies with chronology to assemble the tree of life.Frontiers in bioinformatics · 2025Article
- wQFM-TREE: highly accurate and scalable quartet-based species tree inference from gene trees.Bioinformatics advances · 2025Article
- Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria.Molecular biology and evolution · 2024Article
- Article
- Reply to Springer and Gatesy: The impact of long branches and misalignments on phylogenetic analysis is minimal.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A new phylogeny for Aves is compromised by pervasive misalignment and homology problems.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review.Foods (Basel, Switzerland) · 2024Review
- Generation of accurate, expandable phylogenomic trees with uDance.Nature biotechnology · 2024Article
- Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.The ISME journal · 2024Review
- Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century.Nature communications · 2023Article
- Weighted ASTRID: fast and accurate species trees from weighted internode distances.Algorithms for molecular biology : AMB · 2023Article
- Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data.Bioinformatics (Oxford, England) · 2023Article
- DISCO+QR: rooting species trees in the presence of GDL and ILS.Bioinformatics advances · 2023Article
- Weighting by Gene Tree Uncertainty Improves Accuracy of Quartet-based Species Trees.Molecular biology and evolution · 2022Article
- Reduced and Nonreduced Genomes inmSystems · 2022Article
- Recent progress on methods for estimating and updating large phylogenies.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
16 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIncomplete lineage sorting (ILS), modelled by the multi-species coalescent (MSC), is known to create discordance between gene trees and species trees, and lead to inaccurate species tree estimations unless appropriate methods are used to estimate the species tree. While many statistically consistent methods have been developed to estimate the species tree in the presence of ILS, only ASTRAL-2 and NJst have been shown to have good accuracy on large datasets. Yet, NJst is generally slower and less accurate than ASTRAL-2, and cannot run on some datasets.
resultsWe have redesigned NJst to enable it to run on all datasets, and we have expanded its design space so that it can be used with different distance-based tree estimation methods. The resultant method, ASTRID, is statistically consistent under the MSC model, and has accuracy that is competitive with ASTRAL-2. Furthermore, ASTRID is much faster than ASTRAL-2, completing in minutes on some datasets for which ASTRAL-2 used hours.
conclusionsASTRID is a new coalescent-based method for species tree estimation that is competitive with the best current method in terms of accuracy, while being much faster. ASTRID is available in open source form on github.
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.