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Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Phylogenetic Trees

Phylogenetic Trees

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Mutation, Gene Flow, and Genetic Drift

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Related Experiment Video

Updated: May 18, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

TreeFix: statistically informed gene tree error correction using species trees.

Yi-Chieh Wu¹, Matthew D Rasmussen, Mukul S Bansal

¹Department of Electrical Engineering and Computer Science, Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Systematic Biology

|September 6, 2012

Summary

This summary is machine-generated.

Accurate gene tree reconstruction is challenging with sequence data alone. TreeFix improves gene trees by integrating species tree information, enhancing phylogenetic accuracy for evolutionary studies.

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Area of Science:

Phylogenetics
Computational Biology
Genomics

Background:

Accurate gene tree reconstruction is crucial for understanding gene evolution but is often limited by insufficient sequence data.
Phylogenetic analyses frequently face challenges in confidently resolving gene tree topologies due to data limitations.

Purpose of the Study:

To introduce TreeFix, a novel phylogenetic program designed to enhance gene tree reconstructions.
To present a new framework for integrating sequence data with species tree information to improve phylogenetic accuracy.

Main Methods:

TreeFix implements a framework that combines gene sequence data and species tree information.
The program refines a given gene tree (preferably from maximum likelihood) to find a statistically equivalent tree minimizing a species tree-based cost function.

Main Results:

TreeFix demonstrated significant improvements in gene tree reconstructions compared to state-of-the-art methods.
The program was successfully applied to Drosophila and fungal genome datasets, as well as simulated phylogenies.

Conclusions:

TreeFix offers an accurate, fast, and simple method for improving gene tree reconstructions.
The program has broad applicability and significant implications for future gene evolution research.