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.
Highlights
Advances in high‐throughput sequencing technologies have led to an unprecedented wealth of genome‐scale data for evolutionary analysis
A range of bioinformatics tools and resources are readily available for using codon‐based models of evolution (Pond, Frost, & Muse, 2005; Stern et al, 2007; Valle et al, 2014; Zhang, Wang, Long, & Fan, 2013), the CodeML program in the PAML pack‐ age (Yang, 2007) is among the most widely used
To demonstrate the use of the clade models in the preset running mode in EasyCodeML, we present an analysis of the ECP‐EDN gene family in primates
Summary
Advances in high‐throughput sequencing technologies have led to an unprecedented wealth of genome‐scale data for evolutionary analysis. Ratio is the same across branches of the phylogeny but different among sites in the alignment These codon substitution models are: M0 (one‐ratio), M1a (nearly neutral), M2a (positive selection), M3 (discrete), M7 (beta), M8 (beta and ω > 1) and M8a (beta and ω = 1). To demonstrate the use of the clade models in the preset running mode in EasyCodeML, we present an analysis of the ECP‐EDN gene family in primates. We compare the M8 and M8a models to test for sites under positive selection in the outer membrane protein C (ompC) of strains of Enterobacter aerogenes, this particular model comparison is available in the preset running mode of EasyCodeML. We identified nine codons as being under positive selection with posterior probability >0.95, matching the results of Padhi et al (2009)
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