IMPACT_S: Integrated Multiprogram Platform to Analyze and Combine Tests of Selection

Abstract

Among the major goals of research in evolutionary biology are the identification of genes targeted by natural selection and understanding how various regimes of evolution affect the fitness of an organism. In particular, adaptive evolution enables organisms to adapt to changing ecological factors such as diet, temperature, habitat, predatory pressures and prey abundance. An integrative approach is crucial for the identification of non-synonymous mutations that introduce radical changes in protein biochemistry and thus in turn influence the structure and function of proteins. Performing such analyses manually is often a time-consuming process, due to the large number of statistical files generated from multiple approaches, especially when assessing numerous taxa and/or large datasets. We present IMPACT_S, an easy-to-use Graphical User Interface (GUI) software, which rapidly and effectively integrates, filters and combines results from three widely used programs for assessing the influence of selection: Codeml (PAML package), Datamonkey and TreeSAAP. It enables the identification and tabulation of sites detected by these programs as evolving under the influence of positive, neutral and/or negative selection in protein-coding genes. IMPACT_S further facilitates the automatic mapping of these sites onto the three-dimensional structures of proteins. Other useful tools incorporated in IMPACT_S include Jmol, Archaeopteryx, Gnuplot, PhyML, a built-in Swiss-Model interface and a PDB downloader. The relevance and functionality of IMPACT_S is shown through a case study on the toxicoferan-reptilian Cysteine-rich Secretory Proteins (CRiSPs). IMPACT_S is a platform-independent software released under GPLv3 license, freely available online from http://impact-s.sourceforge.net.

Whole-Genome Identification, Phylogeny, and Evolution of the Cytochrome P450 Family 2 (CYP2) Subfamilies in Birds

“…The number of degrees of freedom (df) was calculated as the difference in the number of estimated parameters between the models ( Yang 2000 ; Wong et al 2004 ). We used the IMPACT_S software to automate these calculations ( Maldonado et al 2014 ).…”

Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions

“…In order to understand how the sites under positive selection, influence the structure and/or function of the mt subunits, we located them in the respective Cephalopoda protein sequence alignment. To perform this, we used the Alignment Filter tool of the IMPACT_S software [ 58 ]. These sites were identified (p-value < 0.05) by the BEB (CODEML branch-site model test) and MEME (DATAMONKEY episodic diversifying selection) analyses.…”

EasyCodeML: A visual tool for analysis of selection using CodeML

“…However, these programs have various limitations, such as complex configuration procedures or a reduced set of codon models. For example, two recently released packages, IDEA (Interactive Display for Evolutionary Analyses; Egan et al, ) and IMPACT_S (Integrated Multiprogram Platform to Analyze and Combine Tests of Selection; Maldonado, et al, ), provide a graphical user interface but only implement three pairs of site models (M0 vs. M3, M1a vs. M2a and M7 vs. M8). Xu and Yang () developed a graphical user interface for PAML named pamlX, but the complex parameter settings for CodeML still remained challenging for users.…”