Related Experiment Video
Updated: Jun 1, 2026
12:00
A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
Rubén Sánchez1, François Serra, Joaquín Tárraga
1Evolutionary Genomics Lab, Bioinformatics and Genomics Department, Centro de Investigación Príncipe Felipe, Autopista del Saler, 16-3, 46013 Valencia, Spain.
Nucleic Acids Research
|June 8, 2011
Summary
Phylemon 2.0 offers an integrated web suite for molecular evolution and phylogenetics. This release aids both experts and non-experts in complex sequence analyses and hypothesis testing.
Area of Science:
- Bioinformatics
- Computational Biology
- Evolutionary Biology
Background:
- Molecular sequence analysis is crucial for understanding evolutionary processes.
- Existing web tools often lack integration, hindering complex analyses.
- There is a growing need for user-friendly yet powerful bioinformatics resources.
Purpose of the Study:
- To introduce Phylemon 2.0, an updated suite of web tools for molecular evolution and phylogenetics.
- To provide an integrated environment for diverse evolutionary analyses, catering to users of all expertise levels.
- To enhance the capabilities for phylogenomic analyses and hypothesis testing.
Main Methods:
- Integration of approximately 30 distinct bioinformatics tools within a single web platform.
- Development of features for sequence alignment, tree reconstruction, visualization, and manipulation.
- Implementation of evolutionary hypothesis testing modules and user-guided analysis pipelines.
Main Results:
- Phylemon 2.0 provides a unified environment for sequence analysis, file management, and result editing.
- The platform offers guided analysis suggestions, simplifying complex workflows for users.
- Users can design and save custom phylogenetic pipelines for multi-gene (phylogenomic) analyses.
Conclusions:
- Phylemon 2.0 significantly enhances the accessibility and efficiency of molecular evolution and phylogenetics research.
- The integrated approach and user-centric design empower a broader range of scientists to perform advanced analyses.
- This updated suite supports comprehensive evolutionary hypothesis testing and phylogenomic studies.
Related Concept Videos
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...
01:23Phylogeny
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...
01:28Microbial Phylogeny
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,...
01:20Applications of Molecular Taxonomy
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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...