February 26, 2016 | Jaime Huerta-Cepas, François Serra, Peer Bork
The Environment for Tree Exploration (ETE) v3 is an advanced computational framework designed to simplify the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Key features of ETE v3 include:
1. **Tree Building**: The *ete-build* tool allows for the unified execution of reproducible phylogenetic workflows, including gene-based and supermatrix-based phylogeny reconstruction. It supports sequence alignment, trimming, substitution model testing, tree inference, and image rendering.
2. **Testing Evolutionary Hypotheses**: The *ete-evol* tool automates CodeML/SLR-based analyses, providing graphical representations of evolutionary models and selective pressures. It supports various models such as site, branch, branch-site, and clade models.
3. **Comparing Trees**: The *ete-compare* tool calculates three measures of tree distance—Robinson-Foulds distance, branch congruence measure, and TreeKO Speciation distance. It handles trees of varying sizes and duplication events, and provides detailed lists of differences and coincidences.
4. **Taxonomy Databases**: The *ete-ncbiquery* tool integrates with the NCBI taxonomy database, enabling efficient queries for extracting taxonomic information, pruned subtrees, and lineage tracks.
5. **Additional Tools**: ETE v3 includes other tools for tasks such as format conversion, topology manipulation, and custom visualization of trees linked to multiple sequence alignments.
ETE v3 offers a comprehensive Python API and command-line tools, making it a versatile and user-friendly framework for phylogenomic analysis and visualization.The Environment for Tree Exploration (ETE) v3 is an advanced computational framework designed to simplify the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Key features of ETE v3 include:
1. **Tree Building**: The *ete-build* tool allows for the unified execution of reproducible phylogenetic workflows, including gene-based and supermatrix-based phylogeny reconstruction. It supports sequence alignment, trimming, substitution model testing, tree inference, and image rendering.
2. **Testing Evolutionary Hypotheses**: The *ete-evol* tool automates CodeML/SLR-based analyses, providing graphical representations of evolutionary models and selective pressures. It supports various models such as site, branch, branch-site, and clade models.
3. **Comparing Trees**: The *ete-compare* tool calculates three measures of tree distance—Robinson-Foulds distance, branch congruence measure, and TreeKO Speciation distance. It handles trees of varying sizes and duplication events, and provides detailed lists of differences and coincidences.
4. **Taxonomy Databases**: The *ete-ncbiquery* tool integrates with the NCBI taxonomy database, enabling efficient queries for extracting taxonomic information, pruned subtrees, and lineage tracks.
5. **Additional Tools**: ETE v3 includes other tools for tasks such as format conversion, topology manipulation, and custom visualization of trees linked to multiple sequence alignments.
ETE v3 offers a comprehensive Python API and command-line tools, making it a versatile and user-friendly framework for phylogenomic analysis and visualization.