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Updated: Jul 5, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Getting a tree fast: Neighbor Joining, FastME, and distance-based methods.

Richard Desper¹, Olivier Gascuel

¹Department of Biology, University College, London, United Kingdom.

Current Protocols in Bioinformatics

|April 23, 2008

Summary

This summary is machine-generated.

Neighbor Joining (NJ) and FastME are fast methods for building phylogenetic trees. FastME offers superior topological accuracy and speed compared to NJ, especially for large datasets.

Related Experiment Videos

Last Updated: Jul 5, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Computational Biology
Bioinformatics
Evolutionary Biology

Background:

Phylogenetic tree construction is crucial for understanding evolutionary relationships.
Distance-based methods offer computational efficiency for large datasets.
Neighbor Joining (NJ) is a popular but less accurate distance-based method.

Purpose of the Study:

To compare the performance of various distance-based phylogenetic tree construction methods.
To highlight the efficiency and accuracy of FastME.
To provide guidance on using distance-based methods, including bootstrapping and sequence alignment.

Main Methods:

Utilized computer simulations to evaluate topological accuracy.
Compared Neighbor Joining (NJ), FastME, BIONJ, WEIGHBOR, and FITCH.
Described evolutionary distance estimation from DNA and protein sequences.
Explained bootstrap analysis for phylogenetic reliability.
Introduced CLUSTAL for sequence alignment and tree generation.

Main Results:

FastME demonstrated the highest topological accuracy among tested distance-based methods.
FastME exhibited superior speed compared to NJ, particularly on large datasets.
NJ showed lower topological accuracy than FastME, FITCH, WEIGHBOR, and BIONJ.
Distance-based methods are effective when molecular clocks are violated or long branches are present.

Conclusions:

FastME is the most efficient and accurate distance-based method for phylogenetic tree construction currently available.
Distance-based methods, especially FastME, are valuable tools for large-scale phylogenetics and bootstrap analysis.
Understanding distance estimation and bootstrapping is essential for reliable phylogenetic inference.