ETE 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


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Maintainer


  • person_outline Jaime Huerta-Cepas <>

Publication for Environment for Tree Exploration

ETE IN pipelines

 (8)
2016
PMCID: 4777378
PMID: 26939122
DOI: 10.1371/journal.pone.0150404

[…] accessed in december, 2014) was used to detect superfamily and multidomain hits in the full length sequences, which regions matching (hhh)2 domain were used to construct the phylogenetic tree. ete 2.2 package was used for the visualization of the tree, the detected domain search hits and supplementary information [17]. the root was placed according to the out-group mammalian (cricetulus […]

2016
PMCID: 4825420
PMID: 26865070
DOI: 10.1093/gbe/evw013

[…] from 1,000 bootstrap replicates. the resulting tree was used to infer and date gene duplication events based on a phylogeny-aware algorithm (huerta-cepas and gabaldón 2011) as implemented in ete v2 (huerta-cepas et al. 2010). this method is complementary to café, which does not consider the topology of the gene tree., in most vertebrates studied to date, or genes are spatially clustered […]

2016
PMCID: 4972966
PMID: 27487948
DOI: 10.1186/s13062-016-0138-1

[…] rooting approach (placing the root at the mid-point of the longest distance between two terminal nodes). visualization of the trees was performed with a python programming language library called ete [60]. additional editing of generated images was done manually using and open source graphics editor inkscape [61]., this is a thorough and sound characterization of retrogenes in the volvox […]

2015
PMCID: 4486849
PMID: 26191053
DOI: 10.3389/fmicb.2015.00661

[…] for bootstrapping. the corresponding neighbor-joining trees were calculated and a consensus tree was produced using the neighbor and consens programs from the phylip package (felsenstein, 1989). ete 2.2 package was used for the visualization of the tree and supplementary information (huerta-cepas et al., 2010)., a secretion signal search was performed in the sequences of dnases […]

2015
PMCID: 4684704
PMID: 26454013
DOI: 10.1093/gbe/evv187

[…] scaffolds (used as reference genome) and all scaffolds of the five isolates of the rice lineage (see supplementary material s6, supplementary material online)., the phylogenetic analysis package ete (huerta-cepas et al. 2010) was used to determine the proportion of different lineages found within the 6,878 topologies analyzed. specifically, we looked for 1) the number of trees where 70-15 […]

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

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Henry Heberle

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Desktop
Great toolkit to work with trees in Python