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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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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...

Microbial Phylogeny

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

Evolution of Microbial Genome

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.

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Updated: Jun 2, 2026

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

PhyleasProg: a user-oriented web server for wide evolutionary analyses.

Joël Busset¹, Cédric Cabau, Camille Meslin

¹INRA, UMR85, Physiologie de la Reproduction et des Comportements, F-37380 Nouzilly, France.

Nucleic Acids Research

|May 3, 2011

Summary

PhyleasProg is a user-friendly web server simplifying evolutionary analyses for biologists. It provides phylogenetic trees and selection data, aiding protein function discovery.

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Last Updated: Jun 2, 2026

A Practical Guide to Phylogenetics for Nonexperts

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Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Evolutionary analyses are crucial in modern biology for understanding sequence function.
High-throughput data necessitates accessible bioinformatics tools for non-specialists.
Existing tools often present usability challenges for researchers lacking specialized expertise.

Purpose of the Study:

To develop PhyleasProg, an intuitive web server for evolutionary analyses.
To provide biologists with a user-friendly tool for robust phylogenetic and selection analyses.
To facilitate the discovery of protein function and structure through integrated bioinformatics approaches.

Main Methods:

Development of a web server (PhyleasProg) with a simple, intuitive interface.
Inputting Ensembl protein IDs and species lists for automated analysis.
Utilizing standard evolutionary methodologies for data computation.

Main Results:

PhyleasProg generates phylogenetic trees and identifies positive/purifying selection.
Results are visualized on protein sequences, 3D structures, and synteny environments.
The server offers a comprehensive suite of evolutionary analysis outputs.

Conclusions:

PhyleasProg democratizes evolutionary analyses for a broader biological audience.
Integrated visualization of phylogenetic and selection data aids in novel biological discoveries.
The tool supports research into protein function, structure, and evolutionary relationships.