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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...
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,...
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 4, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

PHAST and RPHAST: phylogenetic analysis with space/time models.

Melissa J Hubisz1, Katherine S Pollard, Adam Siepel

  • 1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. acs4@cornell.edu

Briefings in Bioinformatics
|February 1, 2011
PubMed
Summary

The PHylogenetic Analysis with Space/Time models (PHAST) software package now has an official v1.0 release, enhancing comparative genomics tools. A new R interface, RPHAST, expands accessibility for statistical and phylogenomic analyses.

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A Practical Guide to Phylogenetics for Nonexperts
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A Practical Guide to Phylogenetics for Nonexperts

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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
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Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

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Related Experiment Videos

Last Updated: Jun 4, 2026

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin

Published on: August 14, 2018

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group
07:49

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

Area of Science:

  • Computational Biology
  • Genomics
  • Bioinformatics

Background:

  • PHAST is a widely used software package for comparative genomics, powering UCSC Genome Browser's Conservation tracks.
  • Developed since 2002, PHAST has been available as provisional software with over 1000 downloads.
  • Existing tools facilitate phylogenetic modeling, functional element identification, and manipulation of genomic data.

Purpose of the Study:

  • To announce the first official release (v1.0) of the PHAST software package.
  • To introduce RPHAST, a new interface for the R statistical computing environment.
  • To highlight improvements in stability, portability, documentation, and new features.

Main Methods:

  • Release of PHAST v1.0 with enhanced stability and features.
  • Development of RPHAST, an R interface to PHAST libraries.
  • Illustrative vignettes demonstrating RPHAST applications in phylogenomics and statistical analysis.

Main Results:

  • PHAST v1.0 offers improved performance and usability for comparative genomics tasks.
  • RPHAST provides accessible integration of PHAST tools within the R environment.
  • RPHAST facilitates complex statistical analyses and rapid prototyping for phylogenomic research.

Conclusions:

  • The official release of PHAST v1.0 and RPHAST v1.0 significantly advances comparative genomics research.
  • RPHAST lowers the barrier for non-C programmers to utilize powerful phylogenetic modeling tools.
  • These releases promote broader application of advanced phylogenomic and statistical analyses in biological research.