Related Experiment Video
Updated: Aug 14, 2026
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
REvolutionH-tl 2.0: A fast and robust tool for decoding evolutionary gene histories
José Antonio Ramírez-Rafael1,2,3, Annachiara Korchmaros2, Katia Aviña-Padilla1
1Department of Genetic Engineering, Center for Research and Advanced Studies of the National Polytechnic Institute, Irapuato Unit, Irapuato, Guanajuato, Mexico.
Plos Computational Biology
|August 12, 2026
Summary
REvolutionH-tl is a novel software platform for evolutionary analyses. It accurately infers gene and species trees, and evolutionary scenarios, outperforming existing tools with integrated visualizations.
Area of Science:
- Comparative genomics
- Evolutionary biology
- Bioinformatics
Background:
- Accurate inference of evolutionary relationships is crucial for understanding genome evolution.
- Existing tools often require multiple steps, external data, or lack integrated visualization capabilities.
Purpose of the Study:
- To develop a fast, scalable, and integrated software platform for inferring orthology relationships, gene trees, species trees, and reconciled evolutionary scenarios.
- To provide a user-friendly tool with built-in visualization for exploring evolutionary dynamics.
Main Methods:
- Utilizes the best match graphs (BMGs) framework for orthogroup and orthologous gene pair prediction.
- Reconstructs event-labeled gene and species trees with integrated reconciliation.
- Benchmarked against established tools using synthetic datasets with known ground truth.
Main Results:
- REvolutionH-tl demonstrates high accuracy in predicting orthologs and evolutionary scenarios.
- Outperforms or matches established tools (e.g., OrthoFinder, RAxML) in accuracy.
- Achieves significantly lower runtimes compared to existing software.
- Offers integrated, publication-ready visualizations for evolutionary data.
Conclusions:
- REvolutionH-tl is a powerful, integrated platform for large-scale evolutionary analyses.
- Combines analytical precision with intuitive interpretability through advanced visualizations.
- Provides a robust, open-source solution for comparative genomics research.
Related Concept Videos
02:05Gene 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...
In contrast, regions which code...
02:05Gene 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...
In contrast, regions which code...
02:54Evolutionary 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...
02:37Gene Duplication and Divergence
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
01:08Evolution 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.
02:35What is Evolutionary History?
Scientists record evolutionary history by analyzing fossil, morphological, and genetic data. The fossil record documents the history of life on Earth and provides evidence for evolution. However, both fossil and living organisms offer evidence that outlines Earth’s evolutionary history.Phylogenetic trees illustrate the evolutionary relationships among these organisms. Scientists infer organisms’ common ancestry by evaluating shared morphological and genetic characteristics. Together, the fossil...