About the ETE Toolkit
The ETE Toolkit was originally
developed at the bioinformatics department of CIPF (Valencia, Spain), and greatly improved
at the comparative genomics group of CRG (Barcelona, Spain) and the Structural and Computational Biology unit of EMBL (Heidelberg, Germany).
At present, ETE is maintained by the Comparative Genomics and Metagenomics group at CBGP (Madrid, Spain).
Citation:
ETE 3: Reconstruction, analysis and visualization of phylogenomic data.
Jaime Huerta-Cepas, Francois Serra and Peer Bork.
Mol Biol Evol 2016; doi: 10.1093/molbev/msw046
Contact:: jhcepas@gmail.com
Older references:
Jaime Huerta-Cepas, Joaquín Dopazo and Toni Gabaldón. ETE: a python Environment for Tree Exploration. BMC Bioinformatics 2010, 11:24.
doi:10.1186/1471-2105-11-24
Highlighted Tools Using ETE
- EggNOG (orthology database)
- PhylomeDB (phylogenetic database)
- Polyphony (3D structures comparsion)
- Phylemon (phylogenetic tools)
- Species delimitation (method)
- TreeKO (duplication aware method to compare trees)
- AGP (Alignment-Free Genome Phylogenies)
- ITEP (exploration of microbial pan-genomes)
- T-RMSD (protein structural classification)
- CanSNPer (genotype classifier of clonal pathogens)
- ReproPhylo (reproducible phylogenetic analyses)
- Avocado (Linux automated testing of tools)
- StreptomeDB 2.0 a database of natural products produced by streptomycetes
- IQ-TREE web server: fast and accurate phylogenetic trees under maximum likelihood.
Related Links and Resources
- A brief introduction to ETE and its programmatic tree visualization features at the SciPy conference (2015)
- A little comparison on how to handle phylogenetic trees in R vs Python (ClimateEcology blog)
- Several ways of displaying data associated with phylogenetic trees (Bacpathgenomics blog)
- Parsing a list of words with ETE to build a Trie (StackOverflow)
- Annotating trees with data: Holt lab scripts
- Guided ete3 API examples (E.Noutahi blog)
- Using ete3 API to plot trees with alignments (Avrilomics blog)