ArticleNucleic acids research2014
Selectome update: quality control and computational improvements to a database of positive selection.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
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- Harmonized cross-species cell atlases of trigeminal and dorsal root ganglia.bioRxiv : the preprint server for biology · 2023Article
- Insights into the Genomics of Clownfish Adaptive Radiation: The Genomic Substrate of the Diversification.Genome biology and evolution · 2023Article
- Phospholipid Scramblase 4 (PLSCR4) Regulates Adipocyte Differentiation via PIP3-Mediated AKT Activation.International journal of molecular sciences · 2022Article
- Convergent consequences of parthenogenesis on stick insect genomes.Science advances · 2022Article
- Relative model selection of evolutionary substitution models can be sensitive to multiple sequence alignment uncertainty.BMC ecology and evolution · 2021Article
- Comparable Number of Genes Having Experienced Positive Selection among Great Ape Species.Animals : an open access journal from MDPI · 2021Article
- The Evolutionary History of Vertebrate Adhesion GPCRs and Its Implication on Their Classification.International journal of molecular sciences · 2021Article
- Harnessing machine learning to guide phylogenetic-tree search algorithms.Nature communications · 2021Article
- Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.Genome biology and evolution · 2021Article
- Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.PloS one · 2021Article
- Directional divergence of Ep300 duplicates in teleosts and its implications.BMC evolutionary biology · 2020Article
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
- Ancient Evolutionary Origin of Intrinsically Disordered Cancer Risk Regions.Biomolecules · 2020Article
- Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC evolutionary biology · 2020Article
- Equiprobable discrete models of site-specific substitution rates underestimate the extent of rate variability.PloS one · 2020Article
- Article
- Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.Molecular biology and evolution · 2019Article
- Simultaneous Bayesian inference of phylogeny and molecular coevolution.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Selectome (http://selectome.unil.ch/) is a database of positive selection, based on a branch-site likelihood test. This model estimates the number of nonsynonymous substitutions (dN) and synonymous substitutions (dS) to evaluate the variation in selective pressure (dN/dS ratio) over branches and over sites. Since the original release of Selectome, we have benchmarked and implemented a thorough quality control procedure on multiple sequence alignments, aiming to provide minimum false-positive results. We have also improved the computational efficiency of the branch-site test implementation, allowing larger data sets and more frequent updates. Release 6 of Selectome includes all gene trees from Ensembl for Primates and Glires, as well as a large set of vertebrate gene trees. A total of 6810 gene trees have some evidence of positive selection. Finally, the web interface has been improved to be more responsive and to facilitate searches and browsing.
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