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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...

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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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Updated: Jul 5, 2026

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.

Matthew Goode¹, Allen G Rodrigo

¹Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand.

Current Protocols in Bioinformatics

|April 23, 2008

Summary

PEBBLE is a new bioinformatics application for phylogenetic analysis. It infers evolutionary relationships and substitution rates, particularly for time-calibrated sequences like viral or ancient DNA.

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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
Evolutionary Biology
Computational Biology

Background:

Phylogenetic analysis is crucial for understanding evolutionary relationships.
Analyzing time-calibrated sequences presents unique computational challenges.
Existing tools may lack flexibility for diverse phylogenetic applications.

Purpose of the Study:

Introduce the PEBBLE (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) application.
Demonstrate PEBBLE's utility for analyzing sequences with varying sampling times.
Provide protocols for phylogenetic tree inference and substitution rate estimation.

Main Methods:

Utilizes the sUPGMA algorithm for phylogenetic tree construction.
Employs maximum likelihood for inferring substitution rate parameters.
Includes protocols for sequence analysis, simulation, and general application use.

Main Results:

PEBBLE successfully implements procedures for time-calibrated sequence analysis.
The application facilitates phylogenetic tree inference and rate estimation.
Demonstrates capabilities for sequence simulation and general bioinformatics workflows.

Conclusions:

PEBBLE offers a customizable and versatile platform for phylogenetic and evolutionary analyses.
The application is particularly suited for handling rapidly evolving or ancient DNA sequences.
PEBBLE enhances bioinformatics capabilities for molecular evolution research.