SICLE: A high-throughput tool for extracting evolutionary relationships from phylogenetic trees

TL;DR

SICLE is a high-throughput command line tool that efficiently extracts and summarizes evolutionary relationships from phylogenetic trees, aiding rapid analysis of complex phylogenetic data.

Contribution

This paper introduces SICLE, a novel, easy-to-use software that integrates into phylogenetic pipelines to identify and quantify evolutionary relationships from large phylogenetic datasets.

Findings

Identified 13 unique sister relationships for Salinibacter ruber.

Most phylogenies showed S. ruber grouping with Bacteriodetes.

Detected 91 phylogenies suggesting possible horizontal gene transfer.

Abstract

We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high- throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/.