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Related Concept Videos

Survival Tree01:19

Survival Tree

Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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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...
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...
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...
Basic Plant Anatomy: Roots, Stems, and Leaves02:27

Basic Plant Anatomy: Roots, Stems, and Leaves

The primary organs of vascular plants are roots, stems, and leaves, but these structures can be highly variable, adapted for the specific needs and environment of different plant species.

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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

A reference guide for tree analysis and visualization.

Georgios A Pavlopoulos1, Theodoros G Soldatos1, Adriano Barbosa-Silva2

  • 1Structural and Computational Biology Unit, EMBL, Meyerhofstrasse 1, Heidelberg, Germany.

Biodata Mining
|February 24, 2010
PubMed
Summary
This summary is machine-generated.

High-throughput biological data is rapidly expanding, making visualization challenging. This review explores current tools for visualizing large biological trees and discusses future development needs for better data analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Vast amounts of data are generated by high-throughput technologies (e.g., microarrays, OMICS).
  • Sequencing costs are decreasing, enabling large-scale evolutionary studies.
  • Rapid database expansion complicates data organization and analysis.

Purpose of the Study:

  • To review current tools for visualizing biological trees and analysis.
  • To identify limitations and potential future developments in tree visualization software.
  • To focus on freely available software for biological data analysis.

Main Methods:

  • Review of visualization tools developed in the last decade.
  • Description of standard computer-readable formats for tree hierarchies.
  • Analysis of tool functionality, limitations, and user-friendliness.

Main Results:

  • Many current visualization tools project data in 2D and lack interactivity.
  • Existing phylogenetic tree tools struggle with large datasets (e.g., > few thousand nodes).
  • Focus on freely available software with diverse tree representation methods.

Conclusions:

  • There is a need for improved, user-friendly, and interactive visualization tools for large biological datasets.
  • Integration with various data sources is crucial for future tool development.
  • Freely available software offers valuable methodologies for biological data analysis.