ArticleBMC bioinformatics2010
JCoDA: a tool for detecting evolutionary selection.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 53 citations in OpenAlex.
- Article
- AlexandrusPS: A User-Friendly Pipeline for the Automated Detection of Orthologous Gene Clusters and Subsequent Positive Selection Analysis.Genome biology and evolution · 2023Article
- FREEDA: An automated computational pipeline guides experimental testing of protein innovation.The Journal of cell biology · 2023Article
- Article
- Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions.Molecular biology and evolution · 2022Article
- GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level.G3 (Bethesda, Md.) · 2020Article
- DGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes.Nucleic acids research · 2020Article
- Under-the-Radar Dengue Virus Infections in Natural Populations of Aedes aegypti Mosquitoes.mSphere · 2020Article
- Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.BMC genomics · 2020Article
- Abundance, Functional, and Evolutionary Analysis of Oxalyl-Coenzyme A Decarboxylase in Human Microbiota.Frontiers in microbiology · 2020Article
- Article
- Characterization of antibiotic resistance genes in the species of the rumen microbiota.Nature communications · 2019Article
- One prophage WO gene rescues cytoplasmic incompatibility inProceedings of the National Academy of Sciences of the United States of America · 2018Article
- Mechanistic insights into molecular evolution of species-specific differential glycosaminoglycan binding surfaces in growth-related oncogene chemokines.Royal Society open science · 2017Article
- PosiGene: automated and easy-to-use pipeline for genome-wide detection of positively selected genes.Nucleic acids research · 2017Article
- Rhodopsin gene copies in Japanese eel originated in a teleost-specific genome duplication.Zoological letters · 2017Article
- LMAP: Lightweight Multigene Analyses in PAML.BMC bioinformatics · 2016Article
- Diversification and coevolution of the ghrelin/growth hormone secretagogue receptor system in vertebrates.Ecology and evolution · 2016Article
- Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi.BMC genomics · 2015Article
- POTION: an end-to-end pipeline for positive Darwinian selection detection in genome-scale data through phylogenetic comparison of protein-coding genes.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences.
resultsJCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway.
conclusionsJCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.
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Registered trials
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.