ArticleGigaScience2020
halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora).Genome biology and evolution · 2026Article
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome.Molecular biology and evolution · 2025Article
- Combining Machine Learning and Multiplexed,bioRxiv : the preprint server for biology · 2025Article
- Allelic variation and duplication of the dmrt1 were associated with sex chromosome turnover in three representative Scatophagidae fish species.Communications biology · 2025Article
- GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions.Bioinformatics (Oxford, England) · 2025Article
- Scaffolded and annotated nuclear and organelle genomes of the North American brown algaFrontiers in genetics · 2025Article
- Genomic Anatomy of Homozygous XX Females and YY Males Reveals Early Evolutionary Trajectory of Sex-determining Gene and Sex Chromosomes in Silurus Fishes.Molecular biology and evolution · 2024Article
- Evolution repeats itself in replicate long-term studies in the wild.Science advances · 2024Article
- Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds.Genome biology and evolution · 2024Article
- Integration of fluorescence in situ hybridization and chromosome-length genome assemblies revealed synteny map for guinea pig, naked mole-rat, and human.Scientific reports · 2023Article
- Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes).The Journal of heredity · 2023Article
- Complex evolutionary processes maintain an ancient chromosomal inversion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Chromosome-Length Assembly of the Baikal Seal (Genes · 2023Article
- An Approximate Bayesian Computation Approach for Modeling Genome Rearrangements.Molecular biology and evolution · 2022Article
- Segmental duplications and their variation in a complete human genome.Science (New York, N.Y.) · 2022Article
- halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.GigaScience · 2020Article
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6 authors.
Funding
Abstract
backgroundLarge-scale sequencing projects provide high-quality full-genome data that can be used for reconstruction of chromosomal exchanges and rearrangements that disrupt conserved syntenic blocks. The highest resolution of cross-species homology can be obtained on the basis of whole-genome, reference-free alignments. Very large multiple alignments of full-genome sequence stored in a binary format demand an accurate and efficient computational approach for synteny block production.
findingshalSynteny performs efficient processing of pairwise alignment blocks for any pair of genomes in the alignment. The tool is part of the HAL comparative genomics suite and is targeted to build synteny blocks for multi-hundred-way, reference-free vertebrate alignments built with the Cactus system.
conclusionshalSynteny enables an accurate and rapid identification of synteny in multiple full-genome alignments. The method is implemented in C++11 as a component of the halTools software and released under MIT license. The package is available at https://github.com/ComparativeGenomicsToolkit/hal/.
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