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Phylogenetic Trees

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.

Evolutionary Relationships through Genome Comparisons

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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...

Phylogeny

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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.

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Updated: Sep 11, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Distances Between Extension Spaces of Phylogenetic Trees.

Maria Alejandra Valdez Cabrera, Amy D Willis

IEEE Transactions on Computational Biology and Bioinformatics

|August 14, 2025

Summary

Analyzing evolutionary relationships between organisms is crucial. This study introduces a new distance metric and algorithm for comparing phylogenetic trees with different gene sets, enhancing evolutionary divergence analysis.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

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The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

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Last Updated: Sep 11, 2025

A Practical Guide to Phylogenetics for Nonexperts

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

The ITS2 Database

The ITS2 Database

Published on: March 12, 2012

Area of Science:

Evolutionary Biology
Bioinformatics
Computational Biology

Background:

Phylogenetic trees are essential for understanding evolutionary relationships.
Existing methods like the BHV metric space are limited to trees with identical leaf sets.
Analyzing gene trees with non-identical leaf sets is challenging due to limited analytical tools.

Purpose of the Study:

To develop a generalized method for comparing phylogenetic trees with non-identical leaf sets.
To introduce a novel distance metric and computational algorithm for this purpose.
To enable broader analysis of evolutionary divergence across different genes and species.

Main Methods:

Defined a distance metric as the shortest BHV distance between extension spaces of trees.
Developed a reduced gradient algorithm for computing this distance.
Assessed the scalability of the algorithm.

Main Results:

Successfully computed distances between phylogenetic trees with non-identical leaf sets.
Demonstrated the algorithm's scalability.
Applied the method to analyze gene trees across multiple domains of life.

Conclusions:

The new distance metric and algorithm provide a general and interpretable approach to analyzing evolutionary divergence.
This method overcomes limitations of previous approaches for trees with non-identical leaf sets.
Enables more comprehensive comparative analyses of gene and species evolution.