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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...
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...
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...
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...
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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Updated: Jun 6, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

iGTP: a software package for large-scale gene tree parsimony analysis.

Ruchi Chaudhary1, Mukul S Bansal, André Wehe

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

BMC Bioinformatics
|November 25, 2010
PubMed
Summary
This summary is machine-generated.

Gene tree parsimony (GTP) software, iGTP, now efficiently infers species phylogenies from thousands of genes and hundreds of taxa. This tool handles gene duplication, loss, and deep coalescence, overcoming limitations of previous methods.

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Last Updated: Jun 6, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

The ITS2 Database
16:17

The ITS2 Database

Published on: March 12, 2012

Area of Science:

  • Genomics
  • Computational Biology
  • Evolutionary Biology

Background:

  • Genomic data enables large-scale phylogenetic analysis.
  • Gene tree incongruence from duplication, loss, incomplete lineage sorting, and horizontal gene transfer complicates species phylogeny inference.
  • Gene tree parsimony (GTP) infers species trees by minimizing evolutionary events.

Purpose of the Study:

  • To introduce iGTP, a software for efficient species tree inference using gene tree parsimony.
  • To overcome performance and functional limitations of existing GTP software.

Main Methods:

  • Implementation of state-of-the-art algorithms for accelerated species tree inference.
  • Incorporation of reconciliation costs for duplication, duplication-loss, and deep coalescence.
  • Development of advanced features including stepwise leaf addition for initial trees and support for unrooted gene trees.

Main Results:

  • iGTP significantly enhances the speed and functionality of gene tree parsimony analyses.
  • The software handles large datasets with thousands of genes and hundreds of taxa.
  • iGTP offers a user-friendly graphical interface with integrated tree visualization.

Conclusions:

  • iGTP facilitates unprecedentedly large-scale gene tree parsimony analyses.
  • The software supports key evolutionary reconciliation costs (duplication, duplication-loss, deep coalescence).
  • iGTP provides a convenient graphical user interface for complex phylogenetic analyses.