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

By Jaime Huerta-Cepas, François Serra, Peer Bork. 2016

2,004 citations recorded by the source corpus.

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

Subfields: Ecology, Evolution, Behavior and Systematics, Genetics, Molecular Biology

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Citations in the corpus

Uniclust databases of clustered and deeply annotated protein sequences and alignments (2016, background): “The cluster page shows (Figure 1): (i) an interactive BioJS alignment viewer (19), which displays our Pfam, SCOP, and PDB annotations as colored bars on top; (ii) an expandable taxonomic tree (20) of the species represented in the Figure 1.”
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, background): “1 (34), which integrates the complete pipeline as a built in gene-tree workflow (code name ‘eggnog50 full’).”
AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential (2019, methodology): “These groupings were also used to validate generated trees by checking if related genomes clade together on tree branches; this was done by using the Environment for Tree Exploration (ETE3) python library (45) to identify the largest monophyletic group (strictly homogeneous) for each ANI clan.”
Covasim: An agent-based model of COVID-19 dynamics and interventions (2020, methodology): “Complete transmission trees for a small network under three different intervention scenarios are shown in Figure 11, visualized via the ETE Toolkit (Huerta-Cepas et al., 2016).”
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper (2016, methodology): “For this, building on latest improvements made to the eggNOG database (Huerta-Cepas et al. 2016b), we have created eggNOG-mapper, an application intended for fast functional annotation of novel sequences.”
ggtreeExtra: Compact Visualization of Richly Annotated Phylogenetic Data (2021, neutral): “Over the past decade, several packages and web tools have been developed to integrate external data into phylogenetic trees, such as iTOL (Letunic and Bork 2019), Evolview (Subramanian et al. 2019), Microreact (Argim on et al. 2016), ETE3 (Huerta-Cepas et al. 2016), and GraPhlAn (Asnicar et al. 2015”
Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination (2021, positive): “The resulting lineage structures were visualized with ete3 (52).”
mRNA Vaccines Induce Durable Immune Memory to SARS-CoV-2 and Variants of Concern (2021, methodology): “ete3 (62) was used to visualize the lineages where each node represents a unique sequence, the size of a node represents its relative copy number fraction in the clone, and the integer next to each node represents the number of mutations from the preceding vertical node.”
OMA standalone: orthology inference among public and custom genomes and transcriptomes (2018, background): “Some of the best established orthology resources include EggNOG (Huerta-Cepas et al., 2016) , Ensembl Compara (Zerbino et al., 2018) , Inparanoid (Sonnhammer and Östlund, 2015) , MBGD (Uchiyama et al., 2012) , OrthoDB (Zdobnov et al., 2017) , OrthoMCL (Chen et al., 2006) , Panther (Mi et al., 2017) ”
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation (2021, background): “Nowadays, various software packages offer additional tree annotation features, both online and as stand-alone packages or libraries, for example ETE toolkit (4), ggtree (5), Dendroscope (6), PhyD3 (7) or Evolview (8).”
Interactive Tree Of Life (iTOL) v4: recent updates and new developments (2019, background): “Nowadays, various other software packages offer additional tree annotation features, both online and as standalone packages, for example ETE toolkit (6), Dendroscope (7) or Evolview (8).”