ArticleEcology and evolution2019
EasyCodeML: A visual tool for analysis of selection using CodeML.
Article in Ecology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 281 papers, 1 of them a synthesis that pooled it.
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Who cites it
281 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of major histocompatibility complex (MHC) class IIA reveals polymorphism and positive selection in many vertebrate species.Molecular ecology · 2022Pooled it
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- Comparative plastome analyses reveal life-form-associated selection signatures in Orchidaceae.BMC plant biology · 2026Article
- Plastome evolution and phylogenomics of Glycine (Leguminosae: Papilionoideae).BMC plant biology · 2026Article
- Retrotransposition Events Shape the Evolution of the Ataxin-3 Gene Family in Primates.Genome biology and evolution · 2026Article
221 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genomic signatures of positive selection and evolutionary constraints can be detected by analyses of nucleotide sequences. One of the most widely used programs for this purpose is CodeML, part of the PAML package. Although a number of bioinformatics tools have been developed to facilitate the use of CodeML, these have various limitations. Here, we present a wrapper tool named EasyCodeML that provides a user-friendly graphical interface for using CodeML. EasyCodeML has a custom running mode in which parameters can be adjusted to meet different requirements. It also offers a preset running mode in which an evolutionary analysis pipeline and publication-quality tables can be exported by a single click. EasyCodeML allows visualized, interactive tree labelling, which greatly simplifies the use of the branch, branch-site, and clade models of selection. The program allows comparison of major codon-based models for analyses of selection. EasyCodeML is a stand-alone package that is supported in Windows, Mac, and Linux operating systems, and is freely available at https://github.com/BioEasy/EasyCodeML.
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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.