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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.
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.
Evolutionary Relationships through Genome Comparisons02:54

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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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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.
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both extant and...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

STRAW: Species TRee Analysis Web server.

Timothy I Shaw1, Zheng Ruan, Travis C Glenn

  • 1Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.

Nucleic Acids Research
|May 11, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces STRAW, a web server for species tree reconstruction using popular coalescent methods. STRAW aids in analyzing multilocus data to infer evolutionary relationships.

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Area of Science:

  • Computational Biology
  • Phylogenetics
  • Bioinformatics

Background:

  • Coalescent methods are widely used for species tree reconstruction due to their ability to handle complex evolutionary scenarios.
  • Existing tools may lack integrated workflows for multiple species tree inference methods.
  • Multilocus sequence data is crucial for accurate phylogenetic analyses.

Purpose of the Study:

  • To present STRAW, a novel web server designed for species tree reconstruction.
  • To offer integrated workflows for three prominent coalescent-based methods: MP-EST, STAR, and NJst.
  • To provide comprehensive analysis outputs including species trees, distance metrics, and visualizations.

Main Methods:

  • Input: Rooted gene trees for STAR and MP-EST; unrooted gene trees for NJst.
  • Utilizes three distinct species tree reconstruction algorithms: MP-EST, STAR, and NJst.
  • Web server implementation for accessible and reproducible phylogenetic analysis.

Main Results:

  • The STRAW web server successfully implements MP-EST, STAR, and NJst for species tree inference.
  • Outputs include the estimated species tree topology.
  • Provides modified Robinson-Foulds distances and tree visualizations for comparative analysis.

Conclusions:

  • STRAW offers a user-friendly platform for species tree reconstruction using coalescent methods.
  • Facilitates the analysis of multilocus data for inferring species phylogenies.
  • Enhances comparative phylogenetics through integrated visualization and distance metrics.