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Phylogeny

Phylogeny

Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.

Phylogenetic Trees

Phylogenetic Trees

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.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Ligand Binding and Linkage

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...

Synteny and Evolution

Synteny and Evolution

John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...

Pedigree Analysis

Pedigree Analysis

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Updated: Jun 22, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyloJS: Bridging phylogenetics and web development with a JavaScript utility library.

Leo A Featherstone¹, Wytamma Wirth¹

¹Peter Doherty Institute for Infection and Immunity University of Melbourne Melbourne Victoria Australia.

Ecology and Evolution

|June 27, 2024

Summary

This summary is machine-generated.

PhyloJS is a new JavaScript library for parsing, writing, and manipulating phylogenetic trees. This tool efficiently handles large datasets, enabling advanced web-based phylogenetics applications.

Keywords:

JavaScript Phylogenetics Web‐Development

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Area of Science:

Bioinformatics
Computational Biology
Web Development

Background:

JavaScript libraries for phylogenetic tree manipulation often bundle visualization with limited manipulation capabilities and documentation.
Increasingly large phylogenetics datasets necessitate specialized tools for web-based applications.

Purpose of the Study:

Introduce PhyloJS, a lightweight, zero-dependency TypeScript and JavaScript library for phylogenetic tree operations.
Provide a solution for parsing, writing, and manipulating phylogenetic trees with enhanced interoperability.

Main Methods:

Developed PhyloJS as a TypeScript and JavaScript library.
Ensured zero-dependency for easy integration.
Optimized for efficient handling of large phylogenetic trees.

Main Results:

PhyloJS enables modification and data extraction from phylogenetic trees.
The library can process trees with up to 10^6 tips.
Facilitates integration with other phylogenetics and data visualization libraries.

Conclusions:

PhyloJS addresses the need for a robust, interoperable library for web-based phylogenetics.
Its efficiency with large datasets supports the development of next-generation applications.
The library is readily available via npm with comprehensive documentation.