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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

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 kingdom.

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?

Phylogenetic Trees

Phylogenetic Trees

Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.

Multi-species Conserved Sequences

Multi-species Conserved Sequences

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.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...

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Updated: Dec 31, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

LMAP_S: Lightweight Multigene Alignment and Phylogeny eStimation.

Emanuel Maldonado¹, Agostinho Antunes^2,3

¹CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450-208, Porto, Portugal.

BMC Bioinformatics

|January 1, 2020

Summary

Researchers can now automate complex genomic data analysis for evolutionary biology using LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation). This tool streamlines multiple sequence alignment and phylogenetic tree estimation, handling large datasets efficiently.

Keywords:

Accuracy Character coding Consensus High-throughput Multi-core Multigene Multiple sequence alignment Phylogeny Software package Uncertainty

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Last Updated: Dec 31, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

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

Area of Science:

Bioinformatics
Computational Biology
Evolutionary Genomics

Background:

High-throughput sequencing generates vast amounts of genomic data, necessitating efficient analysis tools.
Evolutionary biologists require accurate multiple sequence alignments (MSA) and phylogenetic trees (PT) to study phenotypic diversity and adaptive evolution.
Current workflows for MSA and PT estimation can be time-consuming and prone to errors, especially with large datasets.

Purpose of the Study:

To develop an automated, user-friendly tool for efficient and accurate MSA and PT estimation.
To streamline the preparation of multiple sequence files (MSF) and subsequent analysis steps.
To provide a versatile package for handling extensive genomic datasets in evolutionary studies.

Main Methods:

Introduction of LMAP_S (Lightweight Multigene Alignment and Phylogeny eStimation), a command-line and interactive package.
Automation of MSF preparation, MSA estimation, outlier detection, refinement, consensus building, PT estimation, comparison, and editing.
Development for multi-core workstation environments to process multiple datasets efficiently.

Main Results:

LMAP_S successfully automates and improves the workflow for MSA and PT estimation.
The package efficiently handles an unlimited number of datasets, processing over 20 datasets in testing.
LMAP_S integrates over 25 software tools, offering more than 65 algorithm choices across five stages.

Conclusions:

LMAP_S is a versatile, open-source package for high-throughput estimation of MSAs and PTs from multiple datasets.
It offers unparalleled algorithmic choices for optimizing MSA and PT estimation.
The software facilitates integration into complex bioinformatics pipelines and is freely available.