iHam and pyHam: visualizing and processing hierarchical orthologous groups

By Clément-Marie Train, Miguel Pignatelli, Adrian M. Altenhoff, Christophe Dessimoz. 2018

31 citations recorded by the source corpus.

Abstract Summary The 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’.

Subfields: Genetics, Molecular Biology

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Citations in the corpus

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more (2020, methodology): “To explore the relationships among related HOGs defined at each taxonomic level, we previously introduced the graphical viewer iHam (25).”
Advances and Applications in the Quest for Orthologs (2019, methodology): “For example, pyHam is a python library for handling orthoXML files containing Hierarchical Orthologous Groups (HOGs) (Train et al. 2019).”
Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes (2019, methodology): “The two major components of the pipeline that are responsible for constructing the enhanced phylogenies and calculating probabilistic data structures to represent them are pyHam [24] and Datasketch [25], respectively.”