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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell.

Thomas Junier¹, Evgeny M Zdobnov

¹Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland. thomas.junier@unige.ch

Bioinformatics (Oxford, England)

|May 18, 2010

Summary

This study introduces Unix shell programs for efficient phylogenetic tree processing and visualization. The tools automate common operations and generate high-quality graphics for analysis and presentation.

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Area of Science:

Bioinformatics
Computational Biology
Phylogenetics

Background:

Phylogenetic tree analysis is crucial in evolutionary biology.
Processing and visualizing large phylogenetic datasets can be computationally intensive.
Existing tools may lack automation and versatile output formats.

Purpose of the Study:

To develop a user-friendly suite of Unix shell programs for phylogenetic tree manipulation.
To provide automated and interactive tree processing capabilities.
To enable high-quality visualization of phylogenetic trees for diverse applications.

Main Methods:

Development of a suite of Unix shell programs.
Implementation of frequently-used tree operations.
Generation of tree visualizations in scalable vector graphics (SVG) and ASCII formats.

Main Results:

The programs efficiently process any number of phylogenetic trees of any size.
Automated tree operations are performed without user interaction.
SVG and ASCII graphics are generated for presentation and command-line inspection.

Conclusions:

The presented Unix shell programs offer a powerful and flexible solution for phylogenetic tree analysis.
The tools facilitate high-quality visualization and further editing of tree data.
An implementation of bootscanning for recombination breakpoint detection in viral genomes is included as an example.