ete

ete reconstructs, analyzes, and visualizes phylogenetic trees and multiple sequence alignments to support comparative genomics and phylogenetic research.

Key Features:

• Phylogeny reconstruction: Builds gene-based and supermatrix-based phylogenies.
• Multiple sequence alignment handling: Reconstructs, analyzes, and visualizes multiple sequence alignments.
• Evolutionary model testing and visualization: Tests evolutionary models and provides visualization of model results.
• Tree distance calculations: Calculates distances between trees of varying sizes, including comparisons that account for duplications.
• NCBI Taxonomy integration: Integrates with the NCBI taxonomy database for taxonomic annotation and mapping.
• Standalone analytical tools: Provides a suite of standalone utilities for common comparative genomics and phylogenetics tasks.

Scientific Applications:

• Phylogenetic reconstruction: Reconstruction of gene trees and concatenation/supermatrix-based phylogenies.
• Comparative genomics: Comparative analyses of gene families and species relationships using phylogenies and alignments.
• Evolutionary model assessment: Testing and visualization of evolutionary models to study evolutionary dynamics.
• Tree comparison: Quantifying tree similarities and differences, including analyses that consider gene duplications.
• Taxonomic annotation: Mapping phylogenetic results to NCBI taxonomy for taxon-aware analyses.

Methodology:

Reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments; evolutionary model testing and visualization; tree distance calculations including duplication-aware comparisons; integration with the NCBI taxonomy database.