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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...
Applications of Molecular Taxonomy01:20

Applications 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...

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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

MixtureTree: a program for constructing phylogeny.

Shu-Chuan Chen1, Michael S Rosenberg, Bruce G Lindsay

  • 1School of Mathematical and Statistical Sciences, Arizona State University, Tempe, 85287, USA. scchen@math.asu.edu

BMC Bioinformatics
|May 28, 2011
PubMed
Summary
This summary is machine-generated.

MixtureTree v1.0 reconstructs phylogenetic trees from binary sequence data using a novel mixture model algorithm. This computational tool offers higher efficiency than traditional methods for phylogenetic analysis.

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Phylogenetics

Background:

  • MixtureTree v1.0 is a C++ based Linux program for phylogenetic reconstruction.
  • It utilizes mixture models for binary sequence data, including single-nucleotide polymorphisms (SNPs).
  • The program incorporates a bootstrap procedure with majority-rule consensus.

Purpose of the Study:

  • To introduce MixtureTree v1.0, a new software for phylogenetic tree reconstruction.
  • To provide an efficient computational tool for analyzing binary sequence data.

Main Methods:

  • Implementation of a mixture model algorithm for phylogeny reconstruction.
  • Inclusion of three distinct optimization options for the mixture algorithm.
  • Integration of a bootstrap procedure for robust phylogenetic inference.

Main Results:

  • MixtureTree v1.0 is available as a Linux-based package with source code and a User's Guide.
  • The program's mixture algorithm demonstrates higher efficiency compared to Neighbor-Joining, Maximum Parsimony, and Maximum Likelihood methods.

Conclusions:

  • MixtureTree v1.0 offers an efficient alternative for phylogenetic analysis of binary sequence data.
  • Potential improvements for mixture tree algorithms include addressing time-consuming aspects by employing revised Expectation-Maximization (EM) algorithms.