TreeDist: Phylogenetic Tree Distance Calculations and Visualizations
by Martin R. Smith
Available on 1 platform
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Description
A software tool implementing multiple measures for calculating distances between phylogenetic trees, including information-based generalized Robinson-Foulds distances, Jaccard-Robinson-Foulds distances, and the Nearest Neighbour Interchange distance. It includes tools for visualizing tree space mappings, identifying islands of trees, calculating medians, and computing the information content of trees and splits. The tool is authored by Martin R. Smith and is associated with multiple published methodologies.
Use Cases
Compare phylogenetic tree topologies based on implemented distance measures like Robinson-Foulds variants.
Visualize the structure of tree space based on mapping tools mentioned in the description.
Identify clusters or 'islands' of similar trees within a larger set.
Compute a representative median tree from a collection of phylogenetic trees.
Assess the information content of individual tree splits or entire trees.
Strengths
Implements a wide array of established tree distance metrics from multiple peer-reviewed publications.
Includes supplementary tools for visualization, cluster identification, and median calculation.
Limitations
Row count and dataset scale are unknown, which may limit suitability assessment.
Column-level documentation is absent; field semantics must be inferred after download.
Provenance
Source
Martin R. Smith
Collection Method
Software implementation of published algorithms.
Time Range
null
Freshness
Last update date is unknown; freshness unverified.