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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...
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.
 Building a Survival Tree
Constructing a survival tree begins...
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...
Chi-square Analysis02:46

Chi-square Analysis

The chi-square test is a statistical hypothesis test. It is used to check whether there is a significant difference between an expected value and an observed value. In the context of genetics, it enables us to either accept or reject a hypothesis, based on how much the observed values deviate from the expected values.
The chi-square test was developed by Pearson in 1990.
The first step of performing a Chi-square analysis is to establish a null hypothesis, which assumes that there is no real...

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Related Experiment Video

Updated: Jun 26, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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Maximum parsimony for tree mixtures.

Stefan Grünewald1, Vincent Moulton

  • 1Department of Combinatorics and Geometry, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 YueYang Road, Shanghai 200031. stefan@picb.ac.cn

IEEE/ACM Transactions on Computational Biology and Bioinformatics
|January 31, 2009
PubMed
Summary
This summary is machine-generated.

Phylogenetic tree inference using concatenated sequences can be complex. Parsimony methods struggle with mixtures of trees, leading to NP-complete problems and numerous most parsimonious trees.

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Related Experiment Videos

Last Updated: Jun 26, 2026

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
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A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Phylogenetic tree inference commonly concatenates sequence alignments from multiple genomic loci.
  • Gene duplication and lineage sorting can cause different loci to support conflicting phylogenetic trees, creating "phylogenetic mixtures."
  • Understanding how phylogenetic inference methods handle these mixtures is crucial for accurate evolutionary reconstructions.

Purpose of the Study:

  • To investigate the behavior of parsimony, a popular phylogenetic inference method, when applied to mixtures of two distinct phylogenetic trees.
  • To analyze the computational complexity and the number of optimal solutions for parsimony on tree mixtures.

Main Methods:

  • Theoretical analysis of the parsimony problem applied to mixtures of two trees.
  • Demonstration of NP-completeness for this specific problem.
  • Characterization of the number of most parsimonious trees for certain mixtures.
  • Explicit description of most parsimonious trees and scores for mixtures generated by a single Tree Bisection and Reconnection (TBR) operation.

Main Results:

  • The parsimony problem is NP-complete when inferring trees from mixtures of two distinct trees.
  • Certain mixtures of two trees can result in an exponential number of most parsimonious trees relative to the number of leaves.
  • An explicit description is provided for the most parsimonious trees and their scores when trees are related by a single TBR operation.

Conclusions:

  • Parsimony-based phylogenetic inference is computationally challenging for mixtures of two trees.
  • The presence of gene duplication and lineage sorting can lead to significant ambiguity in phylogenetic reconstruction using parsimony.
  • Further research is needed to develop robust methods for handling phylogenetic mixtures in large-scale genomic analyses.