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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...
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...
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,...

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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

Bosque: integrated phylogenetic analysis software.

Salvador Ramírez-Flandes1, Osvaldo Ulloa

  • 1Departmento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, Chile. sram@profc.udec.cl

Bioinformatics (Oxford, England)
|September 3, 2008
PubMed
Summary
This summary is machine-generated.

Phylogenetic analyses are streamlined with Bosque, a new software integrating sequence alignment, tree editing, and database management. This tool simplifies complex bioinformatics workflows for researchers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Phylogenetic analyses often involve managing diverse file formats and multiple software programs.
  • Existing tools typically rely solely on local resources for computation and file management, leading to inefficiencies.
  • Extended computation times on local machines can hinder research progress.

Purpose of the Study:

  • To develop a comprehensive software solution that addresses the challenges in current phylogenetic analyses.
  • To create a multi-platform client-server system for efficient phylogenetic data processing.
  • To integrate various phylogenetic tasks into a single, user-friendly environment.

Main Methods:

  • Developed 'Bosque', a multi-platform client-server software.
  • Implemented functionalities for sequence alignment and graphical tree visualization/editing.
  • Integrated results into a local relational database for comprehensive management.

Main Results:

  • Bosque provides a unified environment for standard phylogenetic tasks.
  • The software supports both local and remote server-based computations.
  • Efficient integration of all phylogenetic analysis steps, from alignment to tree editing.

Conclusions:

  • Bosque offers a powerful and integrated solution for phylogenetic analyses.
  • The software enhances efficiency by managing diverse data formats and computational demands.
  • Bosque facilitates a more seamless workflow for evolutionary biology research.