ArticleNucleic acids research2011
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 99 papers.
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99 citing papers in PubMed.
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- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- Comparative transcriptomic analysis reveals conserved programmes underpinning organogenesis and reproduction in land plants.Nature plants · 2021Article
- Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes amongJournal of fungi (Basel, Switzerland) · 2021Article
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- Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum.Molecular biology and evolution · 2020Article
- MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.Nucleic acids research · 2020Article
- Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha.Molecular biology and evolution · 2020Article
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- Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence.The Plant journal : for cell and molecular biology · 2020Article
- Evolutionary and functional patterns of shared gene neighbourhood in fungi.Nature microbiology · 2019Article
- Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes.Genetics · 2019Article
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.Nucleic acids research · 2019Article
- Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication.Molecular biology and evolution · 2018Article
- Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa.Genome announcements · 2018Article
- Probing the Phylogenomics and Putative Pathogenicity Genes of Pythium insidiosum by Oomycete Genome Analyses.Scientific reports · 2018Article
- Practical considerations for plant phylogenomics.Applications in plant sciences · 2018Review
- Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.BMC biology · 2018Article
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7 authors.
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Abstract
The growing availability of complete genomic sequences from diverse species has brought about the need to scale up phylogenomic analyses, including the reconstruction of large collections of phylogenetic trees. Here, we present the third version of PhylomeDB (http://phylomeDB.org), a public database for genome-wide collections of gene phylogenies (phylomes). Currently, PhylomeDB is the largest phylogenetic repository and hosts 17 phylomes, comprising 416,093 trees and 165,840 alignments. It is also a major source for phylogeny-based orthology and paralogy predictions, covering about 5 million proteins in 717 fully-sequenced genomes. For each protein-coding gene in a seed genome, the database provides original and processed alignments, phylogenetic trees derived from various methods and phylogeny-based predictions of orthology and paralogy relationships. The new version of phylomeDB has been extended with novel data access and visualization features, including the possibility of programmatic access. Available seed species include model organisms such as human, yeast, Escherichia coli or Arabidopsis thaliana, but also alternative model species such as the human pathogen Candida albicans, or the pea aphid Acyrtosiphon pisum. Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights.
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