ShadowCaster: compositional methods under the shadow of phylogenetic models for the detection of horizontal gene transfer events in prokaryotes.

Abstract

Abstract: Horizontal gene transfer (HGT) plays an important role in the evolution of many organisms, especially in prokaryotes where commonly occurs. Microbial communities can improve survival due to the evolutionary innovations induced by HGT. Thus, HGT detection has been a major focus of evolutionary biologists and several computational approaches have arisen to identify genes horizontally transferred over those vertically inherited from the recipient genomes. This has been proven to be a complex task due to the generation of a great number of false positives and the prediction disagreement among the existing methods. Here, we present ShadowCaster, a hybrid approach that sequentially combines compositional features under the shadow of phylogenetic models independent of tree reconstruction to improve the detection of HTG events in prokaryotes. ShadowCaster s predictions, related to heavy metal resistance in the genome of Rhodanobacter denitrificans, showed the highest agreement and accuracy among the most popular state-of-the-art computational approaches. ShadowCaster is released as an open-source software under the GPLv3 license.