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Related Concept Videos

Microbial Phylogeny01:28

Microbial 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,...
Phylogenetic Trees03:21

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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogenetic Trees03:21

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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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
Phylogeny01:23

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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...
Evolutionary Relationships through Genome Comparisons02:54

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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A Practical Guide to Phylogenetics for Nonexperts
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phyloPipeR: An R Package for End-to-End Phylogenetic Reconstruction and Tree Comparison.

Feifei Li1, Yue Zou1, Tong Li1

  • 1Computational and Integrative Biology Group, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.

Current Issues in Molecular Biology
|June 26, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces phyloPipeR, an R package for automated phylogenetic analysis. It streamlines complex workflows from sequence retrieval to tree comparison, enhancing reproducibility and accessibility for evolutionary studies.

Keywords:
R packagecoalescent analysisphylogenetic reconstructionphylogenomicstree comparisonworkflow integration

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Area of Science:

  • Evolutionary biology
  • Bioinformatics
  • Computational phylogenetics

Background:

  • Phylogenetic reconstruction involves multiple complex, independent tools, hindering reproducibility.
  • Large-scale phylogenetic analyses face significant technical challenges and reproducibility issues.

Purpose of the Study:

  • To present phyloPipeR, an R package offering an integrated, automated framework for phylogenetic analysis.
  • To simplify and enhance the reproducibility of end-to-end phylogenetic workflows.

Main Methods:

  • Developed an R package, phyloPipeR, for automated phylogenetic analysis.
  • Integrated ortholog retrieval, sequence alignment, trimming, tree inference, and tree comparison.
  • Supported modular execution of individual workflow steps.

Main Results:

  • phyloPipeR provides a unified environment for complete phylogenetic workflows.
  • The package implements diverse phylogenetic inference methods and strategies (concatenation, coalescent).
  • Facilitates quantitative tree comparison within the same framework.

Conclusions:

  • phyloPipeR reduces technical barriers and improves reproducibility in phylogenetic analyses.
  • Offers a scalable solution for systematic and integrative evolutionary studies.
  • Enhances accessibility for researchers conducting phylogenetic reconstruction.