ArticleBioinformatics (Oxford, England)2024
Pandagma: a tool for identifying pan-gene sets and gene families at desired evolutionary depths and accommodating whole-genome duplications.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Legume genome structures and histories inferred from Cercis canadensis and Chamaecrista fasciculata genomes.The Plant journal : for cell and molecular biology · 2026Article
- Chromosome-level haplotype-resolved genome assemblies and annotations of Apios americana and Apios priceana.Scientific data · 2026Article
- Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes.bioRxiv : the preprint server for biology · 2025Article
- Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.BMC plant biology · 2025Article
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Authors and funding
4 authors.
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Abstract
summaryIdentification of allelic or corresponding genes (pan-genes) within a species or genus is important for discovery of biologically significant genetic conservation and variation. Similarly, identification of orthologs (gene families) across wider evolutionary distances is important for understanding the genetic basis for similar or differing traits. Especially in plants, several complications make identification of pan-genes and gene families challenging, including whole-genome duplications, evolutionary rate differences among lineages, and varying qualities of assemblies and annotations. Here, we document and distribute a set of workflows that we have used to address these problems.
resultsPandagma is a set of configurable workflows for identifying and comparing pan-gene sets and gene families for annotation sets from eukaryotic genomes, using a combination of homology, synteny, and expected rates of synonymous change in coding sequence. AVAILABILITY AND IMPLEMENTATION: The Pandagma workflows, example configurations, implementation details, and scripts for retrieving public datasets, are available at https://github.com/legumeinfo/pandagma.
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