ArticleGenome research2014
Alignathon: a competitive assessment of whole-genome alignment methods.
Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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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
56 citing papers in PubMed.
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- Accelerating minimap2 for whole-genome alignment.Bioinformatics (Oxford, England) · 2026Article
- INSIG1 parallel substitution drives lipid/sterol metabolic plasticity mediating desert adaptation in ungulates.Communications biology · 2026Article
- Quantifying Hierarchical Conflicts in Homology Statements.Journal of molecular evolution · 2025Article
- HAlign-G: rapid and low-memory multiple-genome aligner for large-scale closely related genomes.Genome biology · 2025Article
- MAFin: motif detection in multiple alignment files.Bioinformatics (Oxford, England) · 2025Article
- Article
- Pangenome graph construction from genome alignments with Minigraph-Cactus.Nature biotechnology · 2024Article
- Hybridisation has shaped a recent radiation of grass-feeding aphids.BMC biology · 2023Article
- AdaLiftOver: high-resolution identification of orthologous regulatory elements with Adaptive liftOver.Bioinformatics (Oxford, England) · 2023Article
- Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.bioRxiv : the preprint server for biology · 2023Article
- Evaluating impacts of syntenic block detection strategies on rearrangement phylogeny using Mycobacterium tuberculosis isolates.Bioinformatics (Oxford, England) · 2023Article
- Multiple genome alignment in the telomere-to-telomere assembly era.Genome biology · 2022Review
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Genomic signatures of high-altitude adaptation and chromosomal polymorphism in geladas.Nature ecology & evolution · 2022Article
- Genome-Wide Reconstruction of Rediploidization Following Autopolyploidization across One Hundred Million Years of Salmonid Evolution.Molecular biology and evolution · 2022Article
- Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model.Bioinformatics advances · 2022Article
- A near complete genome for goat genetic and genomic research.Genetics, selection, evolution : GSE · 2021Article
- nf-LO: A Scalable, Containerized Workflow for Genome-to-Genome Lift Over.Genome biology and evolution · 2021Article
- CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes.Genomics, proteomics & bioinformatics · 2021Article
Corrections and comments
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Authors and funding
26 authors.
Funding
Abstract
Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.
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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.