ArticleBioinformatics (Oxford, England)2019
iHam and pyHam: visualizing and processing hierarchical orthologous groups.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Genomic Exaptation and Regulatory Landscape Shifts as Key Mechanisms Enabling Flatworm Terrestrialization.Genome biology and evolution · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.Journal of molecular evolution · 2025Article
- EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.Nature ecology & evolution · 2025Article
- The distinct roles of genome, methylation, transcription, and translation on protein expression in Arabidopsis thaliana resolve the Central Dogma's information flow.Genome biology · 2025Article
- An episodic burst of massive genomic rearrangements and the origin of non-marine annelids.Nature ecology & evolution · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
- Chromosome-level genome assembly of Iodes seguinii and its metabonomic implications for rheumatoid arthritis treatment.The plant genome · 2025Article
- Orthology inference at scale with FastOMA.Nature methods · 2025Article
- Adaptive genomic plasticity in large-genome, broad-host-range vibrio phages.The ISME journal · 2025Article
- Comparative Genomics and the Salivary Transcriptome of the Redbanded Stink Bug Shed Light on Its High Damage Potential to Soybean.Genome biology and evolution · 2024Article
- OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.Nucleic acids research · 2024Article
- A panoramic view of the genomic landscape of the genusMicrobial genomics · 2023Article
- Identification of hidden associations among eukaryotic genes through statistical analysis of coevolutionary transitions.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Repeated truncation of a modular antimicrobial peptide gene for neural context.PLoS genetics · 2022Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.Genome biology and evolution · 2021Article
- Positive selection and gene duplications in tumour suppressor genes reveal clues about how cetaceans resist cancer.Proceedings. Biological sciences · 2021Article
- OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more.Nucleic acids research · 2021Article
- Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes.PLoS computational biology · 2020Article
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4 authors.
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Abstract
summaryThe evolutionary history of gene families can be complex due to duplications and losses. This complexity is compounded by the large number of genomes simultaneously considered in contemporary comparative genomic analyses. As provided by several orthology databases, hierarchical orthologous groups (HOGs) are sets of genes that are inferred to have descended from a common ancestral gene within a species clade. This implies that the set of HOGs defined for a particular clade correspond to the ancestral genes found in its last common ancestor. Furthermore, by keeping track of HOG composition along the species tree, it is possible to infer the emergence, duplications and losses of genes within a gene family of interest. However, the lack of tools to manipulate and analyse HOGs has made it difficult to extract, display and interpret this type of information. To address this, we introduce interactive HOG analysis method, an interactive JavaScript widget to visualize and explore gene family history encoded in HOGs and python HOG analysis method, a python library for programmatic processing of genes families. These complementary open source tools greatly ease adoption of HOGs as a scalable and interpretable concept to relate genes across multiple species. AVAILABILITY AND IMPLEMENTATION: iHam's code is available at https://github.com/DessimozLab/iHam or can be loaded dynamically. pyHam's code is available at https://github.com/DessimozLab/pyHam and or via the pip package 'pyham'.
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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.