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Related Concept Videos

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...
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...

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Related Experiment Video

Updated: Jun 15, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

FastTree 2--approximately maximum-likelihood trees for large alignments.

Morgan N Price1, Paramvir S Dehal, Adam P Arkin

  • 1Physical Biosciences Division, Lawrence Berkeley National Lab, Berkeley, California, United States of America. MorganNPrice@yahoo.com

Plos One
|March 13, 2010
PubMed
Summary
This summary is machine-generated.

FastTree 2 enhances phylogenetic inference for large sequence alignments, improving accuracy with subtree-pruning-regrafting and maximum-likelihood methods. This scalable tool enables rapid construction of large-scale evolutionary trees.

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Last Updated: Jun 15, 2026

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Area of Science:

  • Computational biology
  • Bioinformatics
  • Evolutionary genetics

Background:

  • FastTree is a tool for inferring phylogenies from large sequence alignments.
  • Previous versions handled hundreds of thousands of sequences.

Purpose of the Study:

  • To describe improvements in FastTree that enhance accuracy without compromising scalability.
  • To introduce FastTree 2 with new algorithms and approximations.

Main Methods:

  • FastTree 2 incorporates minimum-evolution subtree-pruning-regrafting (SPRs) and maximum-likelihood nearest-neighbor interchanges (NNIs).
  • It employs heuristics for tree search and the "CAT" approximation for site-specific evolution rates.
  • The study compared FastTree 2 against PhyML 3 for simulated and genuine alignments.

Main Results:

  • FastTree 2 demonstrates slightly improved accuracy compared to standard maximum-likelihood NNIs (PhyML 3).
  • It is significantly faster (100-1,000x) than methods using maximum-likelihood SPRs for large alignments.
  • FastTree 2 successfully inferred phylogenies for over 237,000 16S ribosomal RNAs on a desktop computer.

Conclusions:

  • FastTree 2 enables the inference of maximum-likelihood phylogenies for very large sequence alignments.
  • The tool offers a scalable and accurate solution for phylogenetic analysis.
  • FastTree 2 is freely available for use.