ETE statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

ETE specifications

Information


Unique identifier OMICS_04267
Name ETE
Alternative name Environment for Tree Exploration
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Jaime Huerta-Cepas

Publication for Environment for Tree Exploration

ETE citations

 (7)
call_split

A First Phylogeny of the Genus Dimocarpus and Suggestions for Revision of Some Taxa Based on Molecular and Morphological Evidence

2017
Sci Rep
PMCID: 5532229
PMID: 28751754
DOI: 10.1038/s41598-017-07045-7
call_split See protocol

[…] o the output tree with the help of the SPLITS v.1.0–19 package for R. The PTP method was executed using the best-scoring ML tree produced earlier using RAxML v. 7.2.7, and was run in Python using the Environment for Tree Exploration package. […]

call_split

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins

2016
PMCID: 5200936
PMID: 27998811
DOI: 10.1016/j.gpb.2016.06.003
call_split See protocol

[…] pyout” option. Phylogenetic trees were reconstructed with PhyML using a maximum likelihood approach . The best-fit model was inferred with ProtTest . All the procedures above were conducted using the Environment for Tree Exploration (ETE) pipeline for phylogenetic analysis . To identify genes of endosymbiotic origin that migrated from the chloroplast to the nucleus in Arabidopsis, we searched for […]

call_split

Phylogenetic species delimitation for crayfishes of the genus Pacifastacus

2016
PeerJ
PMCID: 4841241
PMID: 27114875
DOI: 10.7717/peerj.1915
call_split See protocol

[…] web server (http://species.h-its.org/gmyc/). The PTP method was implemented using the best-scoring ML tree based on COI gene produced earlier using RAxML HPC2 v.8.2.4, and was run in Python using the Environment for Tree Exploration package (). […]

library_books

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships

2015
BMC Genomics
PMCID: 4628237
PMID: 26518129
DOI: 10.1186/s12864-015-2091-2

[…] To identify orthologs and paralogs, we used a species-overlap algorithm [] as implemented in the environment for tree exploration (ETE) v2 []. Shortly, this algorithm starts at each seed protein used for generating the tree and traverses it until reaching the root. Each internal node was labeled […]

library_books

Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes

2015
BMC Genomics
PMCID: 4455531
PMID: 26040695
DOI: 10.1186/s12864-015-1566-5

[…] d and evolutionary distances small [,]. The BI phylogenetic trees obtained with MrBayes 3.1 [], described previously, were used as input trees. PTP analyses were run from Python using the ETE (Python Environment for Tree Exploration) package [] for tree manipulation and visualization. […]

call_split

A Good Compromise: Rapid and Robust Species Proxies for Inventorying Biodiversity Hotspots Using the Terebridae (Gastropoda: Conoidea)

2014
PLoS One
PMCID: 4086986
PMID: 25003611
DOI: 10.1371/journal.pone.0102160
call_split See protocol

[…] ponding to speciation and the other to coalescence. The ML phylogeny obtained with RAxML as the input tree was used as described previously, and PTP analysis was run from Python using the ETE (Python Environment for Tree Exploration) package for tree manipulation and visualization. […]

Citations

Looking to check out a full list of citations?

ETE institution(s)
Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain; Bioinformatics Department, Centro de Investigación Príncipe Felipe, València, Spain

ETE review

star_border star_border star_border star_border star_border
star star star star star

Henry Heberle

star_border star_border star_border star_border star_border
star star star star star
Desktop
Great toolkit to work with trees in Python