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Related Concept Videos

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 kingdom.
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.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
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 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.
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

Identifying optimal incomplete phylogenetic data sets from sequence databases.

Changhui Yan1, J Gordon Burleigh, Oliver Eulenstein

  • 1Department of Computer Science, Iowa State University, Ames, IA 50011, USA.

Molecular Phylogenetics and Evolution
|May 10, 2005
PubMed
Summary
This summary is machine-generated.

A new quasi-biclique method efficiently identifies optimal incomplete phylogenetic data sets from large sequence databases. This approach balances missing data with necessary gene and taxon overlap, improving phylogenetic accuracy.

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Last Updated: May 8, 2026

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Published on: August 25, 2018

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • Large sequence databases are crucial for phylogenetic analysis.
  • Identifying optimal data subsets with controlled missing data remains a challenge.

Purpose of the Study:

  • To introduce a novel graph-theoretic method for selecting incomplete data sets from large sequence databases.
  • To enable efficient phylogenetic analysis by optimizing taxon and gene sampling.

Main Methods:

  • The quasi-biclique method, based on graph theory, identifies data sets with specified missing data.
  • The method ensures sufficient overlap among genes and taxa.

Main Results:

  • Demonstrated utility on simulated and real (green plant) sequence data.
  • Significantly increased taxon and gene sampling with minimal added missing data.
  • Simulations showed that limited missing data often yields highly accurate phylogenetic topologies.

Conclusions:

  • The quasi-biclique method is an effective tool for extracting phylogenetic information from large sequence databases.
  • It aids in identifying essential sequences for constructing large-scale phylogenetic datasets.