tqDist

tqDist computes distances between evolutionary trees using triplet and quartet comparisons to quantify topological similarity for phylogenetic analyses.

Key Features:

• Triplet and Quartet Distances: Computes both triplet and quartet distances to quantify tree similarity and dissimilarity.
• Algorithmic Efficiency: Implements optimized algorithms for triplet and quartet calculations with running time dependent on the number of leaves (n) and the minimum tree degree (d).
• Support for Rooted and Unrooted Trees: Handles both rooted and unrooted tree topologies for broad applicability in phylogenetic analyses.
• Programmatic Interfaces: Provides a Python module and an R package for integration into analysis pipelines.

Scientific Applications:

• Phylogenetic Tree Comparison: Quantitatively assesses similarity between different evolutionary trees using triplet and quartet distances.
• Tree Robustness Analysis: Evaluates how changes in data or assumptions affect tree topology by comparing distances across trees.
• Integration into Bioinformatics Workflows: Incorporates tree-distance calculations into larger genomic or computational biology pipelines via Python and R interfaces.

Methodology:

Computes triplet and quartet distances using optimized algorithms; running time depends on the number of leaves (n) and the minimum tree degree (d); supports both rooted and unrooted trees and exposes functionality via a Python module and an R package.