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Updated: Apr 23, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.

Ruchi Chaudhary¹, David Fernández-Baca¹, John Gordon Burleigh¹

¹Department of Biology, University of Florida, Gainesville, FL 32611 and Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

Bioinformatics (Oxford, England)

|October 3, 2014

Summary

This summary is machine-generated.

MulRF is a new software package for phylogenetic analysis using multi-copy gene trees. It efficiently infers species trees by minimizing the Robinson-Foulds distance, aiding in understanding complex evolutionary histories.

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A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Area of Science:

Computational Biology
Phylogenetics
Evolutionary Biology

Background:

Phylogenetic analysis often involves multi-copy gene trees.
Gene tree discordance can arise from multiple evolutionary processes or errors.

Purpose of the Study:

To introduce MulRF, a platform-independent software package for phylogenetic analysis.
To provide a tool for inferring species trees from large collections of gene trees.

Main Methods:

MulRF generalizes the Robinson-Foulds (RF) distance for multi-labeled trees.
It employs a fast tree search algorithm to find the species tree minimizing RF distance.
The software is implemented in C++ with a Java Swing GUI.

Main Results:

MulRF effectively infers species phylogenies from multi-copy gene trees.
The software offers customizable search options and result assessment features.
A user-friendly graphical user interface (GUI) with tree visualization is provided.

Conclusions:

MulRF is a valuable tool for phylogenetic analysis, particularly with large datasets of gene trees.
Its efficiency and generalized distance measure make it suitable for complex evolutionary scenarios.
The platform-independent nature and GUI enhance its usability.