ArticleNucleic acids research2024
OrthoMaM v12: a database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed.
- kamino: fast proteome-wide variant calling for amino acid phylogenomics.Molecular biology and evolution · 2026Article
- Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.Molecular ecology resources · 2026Article
- MKado: a toolkit for McDonald-Kreitman tests of natural selection.G3 (Bethesda, Md.) · 2026Article
- A deep learning-based score to evaluate multiple sequence alignments.Molecular biology and evolution · 2026Article
- Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models.Molecular biology and evolution · 2026Article
- Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria.Molecular ecology resources · 2026Article
- Indirect genomic effects shape cancer risk across species.bioRxiv : the preprint server for biology · 2026Article
- The Vertebrate Genomes Project Phase I: A global reference genome resource.bioRxiv : the preprint server for biology · 2026Article
- Adaptive evolution of endothelial nitric oxide synthase (NOS3) may reduce cetacean susceptibility to decompression sickness.Molecular biology and evolution · 2026Article
- Multiple molecular and cellular properties jointly affect protein and site-specific evolutionary rates.bioRxiv : the preprint server for biology · 2026Article
- Identification and functional assessment of CDSN gene variants associated with horn phenotypes in sheep.BMC genomics · 2026Article
- Reconstructing mammalian lifespan evolution reveals strong phylogenetic effects and lifespan-associated genes.BMC biology · 2026Article
- DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.bioRxiv : the preprint server for biology · 2026Article
- Unifying phylogenetic traversal and deep learning to guide tree exploration.bioRxiv : the preprint server for biology · 2026Article
- Efficient algorithms for simulating sequences along a phylogenetic tree.Bioinformatics (Oxford, England) · 2026Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- Algorithms to reconstruct past indels: The deletion-only parsimony problem.PLoS computational biology · 2025Article
- Functional differences between rodent and human PD-1 linked to evolutionary divergence.Science immunology · 2025Article
- Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals.Proceedings. Biological sciences · 2024Article
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Abstract
To date, the databases built to gather information on gene orthology do not provide end-users with descriptors of the molecular evolution information and phylogenetic pattern of these orthologues. In this context, we developed OrthoMaM, a database of ORTHOlogous MAmmalian Markers describing the evolutionary dynamics of coding sequences in mammalian genomes. OrthoMaM version 12 includes 15,868 alignments of orthologous coding sequences (CDS) from the 190 complete mammalian genomes currently available. All annotations and 1-to-1 orthology assignments are based on NCBI. Orthologous CDS can be mined for potential informative markers at the different taxonomic levels of the mammalian tree. To this end, several evolutionary descriptors of DNA sequences are provided for querying purposes (e.g. base composition and relative substitution rate). The graphical web interface allows the user to easily browse and sort the results of combined queries. The corresponding multiple sequence alignments and ML trees, inferred using state-of-the art approaches, are available for download both at the nucleotide and amino acid levels. OrthoMaM v12 can be used by researchers interested either in reconstructing the phylogenetic relationships of mammalian taxa or in understanding the evolutionary dynamics of coding sequences in their genomes. OrthoMaM is available for browsing, querying and complete or filtered download at https://orthomam.mbb.cnrs.fr/.
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