EasyCodeML: A visual tool for analysis of selection using CodeML

TLDR

Genomic signatures of positive selection and evolutionary constraints are detected by nucleotide sequence analyses, with CodeML from the PAML package being a widely used tool, though existing bioinformatics aids have limitations. The authors introduce EasyCodeML, a wrapper that offers a user‑friendly graphical interface for CodeML. EasyCodeML is a stand‑alone, cross‑platform tool that provides custom and preset running modes, interactive tree labeling, model comparison, and export of publication‑quality tables, all accessible via a graphical interface and freely available on GitHub.

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.