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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...

Phylogeny

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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

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Gene Evolution - Fast or Slow?

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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.
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Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
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Export of Mitochondrial and Chloroplast Genes

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Updated: Jun 27, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

SEGUL: Ultrafast, memory-efficient and mobile-friendly software for manipulating and summarizing phylogenomic

Heru Handika¹, Jacob A Esselstyn¹

¹Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA.

Molecular Ecology Resources

|April 26, 2024

Summary

SEGUL is a new ultrafast and memory-efficient software for phylogenomic data manipulation. It offers command-line and graphical interfaces, minimizing bioinformatics barriers and enabling analysis on inexpensive hardware.

Keywords:

alignment manipulation alignment summary statistics concatenation phylogenomics segul

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Biology

Background:

Phylogenetic studies increasingly involve large datasets requiring significant computational resources.
Existing software often demands advanced command-line skills and substantial hardware.
There is a need for accessible and efficient tools for phylogenomic data analysis.

Purpose of the Study:

To develop an ultrafast and memory-efficient software for common phylogenomic dataset manipulations.
To provide both command-line interface (CLI) and graphical user interface (GUI) options.
To reduce computational and economic barriers in phylogenomics.

Main Methods:

Developed SEGUL, a software leveraging the Rust programming language for high performance.
Created standalone CLI and GUI applications, alongside libraries for Rust, R, and Python.
Ensured native support for Windows, Linux, macOS (including Apple ARM Macs), and mobile OS (iOS, iPadOS, Android).

Main Results:

SEGUL demonstrates fast execution times and low memory footprints across various platforms and dataset sizes.
The GUI version lowers the barrier to entry for phylogenomic analyses.
Efficiency enables analyses on less powerful, inexpensive hardware.

Conclusions:

SEGUL significantly enhances the accessibility and efficiency of phylogenomic data manipulation.
The software democratizes phylogenomics by reducing hardware and expertise requirements.
Mobile OS support facilitates phylogenomics education in resource-limited environments.