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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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Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...

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Updated: May 15, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

snpTree--a web-server to identify and construct SNP trees from whole genome sequence data.

Pimlapas Leekitcharoenphon¹, Rolf S Kaas, Martin Christen Frølund Thomsen

¹National Food Institute, Technical University of Denmark, 2800 Kgs Lyngby, Denmark. pile@food.dtu.dk

|January 4, 2013

Summary

A new online tool, snpTree, simplifies the analysis of single nucleotide polymorphisms (SNPs) from whole genome sequencing (WGS) data. This automatic SNP analysis and phylogenetic tree construction aids infectious disease epidemiology, even for users with limited bioinformatics experience.

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Published on: February 5, 2014

Area of Science:

Genomics
Epidemiology
Bioinformatics

Background:

Whole genome sequencing (WGS) is becoming routine in infectious disease epidemiology.
Differentiating outbreak isolates requires genomic analysis, often using single nucleotide polymorphisms (SNPs).
Current SNP analysis methods lack standardization and require bioinformatics expertise.

Purpose of the Study:

To introduce snpTree, an automated online server for SNP analysis and phylogenetic tree construction.
To provide a user-friendly tool for infectious disease epidemiology using WGS data.

Main Methods:

snpTree utilizes BWA for aligning WGS data (FASTQ) to reference genomes and Nucmer for assembled genomes (FASTA).
Identified SNPs are concatenated and used to construct phylogenetic trees via FastTree and Perl scripts.
The online server is built using HTML, Java, and Python.

Main Results:

snpTree successfully identified SNPs and constructed phylogenetic trees from WGS and assembled genomes.
Evaluation using bacterial WGS datasets (V. cholerae, S. aureus, S. Typhimurium, M. tuberculosis) showed concordant results for raw reads and assembled genomes.
The tool provides automated SNP analysis, though extensive filtering in one case could not be replicated.

Conclusions:

snpTree offers an easy-to-use, rapid, and standardized solution for automatic SNP analysis in epidemiological studies.
The web server is accessible to users with limited bioinformatics experience.
snpTree facilitates WGS data analysis for infectious disease epidemiology.