ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

Jaime Huerta-Cepas,François Serra,Peer Bork

doi:10.1093/molbev/msw046

Abstract

The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org

Highlights

The Environment for Tree Exploration (ETE) is a toolkit developed to facilitate the computation, analysis and visualization of phylogenetic data
Since its first release (Huerta-Cepas et al 2010), ETE has been widely used as a computational framework to perform numerous phylogenomic analyses, including characterizing newly sequenced genomes (Richards et al 2010; Wang et al 2014), extracting information from large sets of phylogenetic trees (Derelle and Lang 2012; Chiapello et al 2015; MarcetHouben and Gabaldon 2015) and developing third party tools and databases (Zhang et al 2013; Huerta-Cepas et al 2014; Szitenberg et al 2015)
We describe the latest version of the software (ETE v3), featuring a significantly improved a comprehensive Python programming library (API) library and a novel collection of standalone tools

Summary

Tree Building

The ete-build tool provides a unified interface to wrap the execution of reproducible phylogenetic workflows, comprising the reconstruction of gene–trees and supermatrix-based species trees. A single command is used to configure and launch complex phylogenetic pipelines, covering sequence alignment, trimming, substitution-model testing, tree inference, and image rendering The supermatrix-based reconstruction mode permits to build and concatenate multiple sequence alignments with ease, simplifying the inference of species trees based on multiple genes. Advanced options allow to automatically switch from aminoacid to nucleotide alignments based on sequence identity, resuming the execution of workflows, or even testing multiple strategies in parallel. A single command line can be used to test several alignment methodologies or phylogenetic inference programs simultaneously, making the tool suitable to run phylogenomic pipelines. ETE-build was recently used to compute over one million phylogenetic trees for the EggNOG v4.5 database (HuertaCepas et al 2016)

Testing Evolutionary Hypotheses

Comparing Trees

Taxonomy Databases

Conclusions