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Updated: Mar 17, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

apex: phylogenetics with multiple genes.

Thibaut Jombart¹, Frederick Archer², Klaus Schliep³

¹Department of Infectious Disease Epidemiology, MRC Centre for Outbreak Analysis and Modelling, School of Public Health, Imperial College London, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.

Molecular Ecology Resources

|July 16, 2016

Summary

This summary is machine-generated.

Phylogenetic incongruence arises from multiple gene sequences. The new R package apex offers tools for analyzing these separate genetic loci, improving phylogenetic research.

Keywords:

r genetics package phylogenies software

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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
Bioinformatics
Evolutionary Biology

Background:

Increasing availability of multi-gene sequence data across diverse organisms (viruses, bacteria, eukaryotes).
Potential for phylogenetic incongruence due to biological and statistical factors when analyzing multiple loci.
Existing R software packages lack adequate data structures for analyzing multiple genes separately.

Purpose of the Study:

Introduce the R package apex to address the need for analyzing multiple genes in phylogenetics.
Provide new object classes and tools for handling, visualizing, and analyzing multi-gene sequence data.
Facilitate the investigation of phylogenetic incongruence.

Main Methods:

Development of the R package apex.
Implementation of novel object classes for DNA and amino acid sequence storage.
Provision of tools for data handling, visualization, and phylogenetic analysis within the R environment.

Main Results:

The apex package extends existing R standards for sequence data.
apex offers convenient functionalities for managing and analyzing multi-gene datasets.
Demonstration of apex package capabilities through a sample dataset analysis.

Conclusions:

The apex package fills a critical gap in R for multi-gene phylogenetic analysis.
apex enhances the ability to investigate phylogenetic incongruence by enabling separate locus examination.
Facilitates more robust phylogenetic reconstruction and comparative analyses.