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Evolutionary Relationships through Genome Comparisons

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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...

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Related Experiment Video

Updated: Jan 9, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

MolEvolvR: A web-app for characterizing proteins using molecular evolution and phylogeny.

Faisal S Alquaddoomi¹, Joseph T Burke^2,3, Lo Sosinski^3,4

¹Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz, Aurora, CO 80045.

Biorxiv : the Preprint Server for Biology

|December 3, 2025

Summary

MolEvolvR is a web app for studying protein evolution. It visualizes molecular evolution across the tree of life, aiding protein function and evolution hypothesis generation.

Keywords:

Comparative genomics Domain architectures Homology Molecular evolution Phylogenetics Protein characterization Web application

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Published on: August 16, 2017

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Last Updated: Jan 9, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

Evolutionary biology
Bioinformatics
Computational biology

Background:

Studying protein evolution reveals conserved domains and lineage-specific adaptations.
Understanding protein domain architecture and phyletic spread is crucial for functional inference.

Purpose of the Study:

To introduce MolEvolvR, a novel web-app for visualizing protein molecular evolution.
To enable researchers to generate testable hypotheses about protein function and evolution using phylogenetic context.

Main Methods:

MolEvolvR accepts diverse protein/domain sequence inputs.
It employs a computational workflow for homolog data and graphical summaries.
Domain-centric searches capture remote homologs missed by full-length searches.

Main Results:

Provides detailed homolog data and dynamic visualizations (phylogenetic trees, MSAs, domain architectures).
Integrates domain architecture evolution with phyletic distribution and co-occurrence patterns.
Visualizes lineage-specific adaptations versus broadly conserved features.

Conclusions:

MolEvolvR offers a powerful, user-friendly interface for computational protein characterization.
It facilitates evolutionary studies across all superkingdoms.
The tool aids in understanding protein function and evolutionary trajectories.