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Related Concept Videos

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

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...
Phylogeny01:23

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...
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,...
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...
Phylogenetic Species Concept in Microbiology01:22

Phylogenetic Species Concept in Microbiology

The phylogenetic species concept (PSC) is a framework used to delineate species based on evolutionary relationships, emphasizing shared ancestry and diagnosable genetic traits. Unlike morphological or biological species concepts, the PSC is particularly advantageous for microbial taxonomy, where traditional reproductive or phenotypic criteria often fall short due to the prevalence of asexual reproduction, minimal morphological differentiation, and widespread horizontal gene transfer among...

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A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Phybase: an R package for species tree analysis.

Liang Liu1, Lili Yu

  • 1Department of Agriculture and Natural resources, Delaware State University, Dover, DE 19901, USA. lliu@desu.edu

Bioinformatics (Oxford, England)
|February 17, 2010
PubMed
Summary
This summary is machine-generated.

Phybase is a new R package for analyzing species trees, offering tools for manipulation, simulation, and estimation. It includes population sizes alongside topology and branch lengths for comprehensive phylogenetic insights.

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Last Updated: Jun 16, 2026

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Area of Science:

  • Evolutionary Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Phylogenetic analysis is crucial for understanding evolutionary relationships.
  • Species trees require comprehensive data including topology, branch lengths, and population sizes.
  • Existing tools may lack integrated functionalities for advanced species tree analysis.

Purpose of the Study:

  • To introduce Phybase, a novel R package designed for species tree analysis.
  • To provide a versatile tool for reading, writing, manipulating, simulating, estimating, summarizing, and plotting species trees.
  • To facilitate the inclusion of population size data in phylogenetic analyses.

Main Methods:

  • Development of an R package named Phybase.
  • Implementation of functions for various species tree operations.
  • Integration of population size data within the species tree structure.

Main Results:

  • Phybase offers a suite of functions for robust species tree analysis.
  • The package supports diverse phylogenetic tasks, from data input to visualization.
  • It enables the incorporation of population genetics information into phylogenetic inference.

Conclusions:

  • Phybase enhances species tree analysis by integrating diverse functionalities and data types.
  • The package serves as a valuable resource for researchers in evolutionary biology and bioinformatics.
  • Availability of Phybase and its supporting materials promotes wider adoption and application.