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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...
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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.
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The “tree of life” describes the evolution of life and the evolutionary relationships between organisms. The root of the tree is the common ancestor to all life on Earth. All other species radiate from this point, much like the branches of a tree. The numerous tips of these branches on the tree of life represent every living, or extant, species. Extinct species, which are species that no longer exist, can be found towards the center of the tree. Currently, these organisms, both...
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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Pandemic-scale phylogenetics.

Cheng Ye1, Bryan Thornlow2,3, Alexander Kramer2,3

  • 1University of California, San Diego; San Diego, CA 92093, USA.

Biorxiv : the Preprint Server for Biology
|December 20, 2021
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Summary
This summary is machine-generated.

The new phylogenetic package addresses challenges in analyzing large-scale SARS-CoV-2 genomic data. It enables real-time tracking of virus evolution and transmission, aiding pandemic response efforts.

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Last Updated: Oct 9, 2025

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Area of Science:

  • Genomics
  • Epidemiology
  • Computational Biology

Background:

  • The COVID-19 pandemic necessitated large-scale genomic surveillance, overwhelming pre-existing phylogenetic analysis tools.
  • Effective genomic surveillance, epidemiology, and contact tracing require robust and scalable phylogenetic methods.

Approach:

  • Developed a novel phylogenetic package with pandemic-specific optimizations and parallelization techniques.
  • Integrated four programs: UShER, matOptimize, RIPPLES, and matUtils for tree maintenance, refinement, and analysis.
  • Utilized high-performance computing for daily updates of a massive SARS-CoV-2 phylogenetic tree.

Key Points:

  • UShER and matOptimize maintain and refine a comprehensive mutation-annotated phylogenetic tree of SARS-CoV-2.
  • UShER and RIPPLES allow individual labs to incorporate new genomes and detect recombination events in real-time.
  • matUtils facilitates rapid querying and visualization of large SARS-CoV-2 phylogenies.

Conclusions:

  • The developed phylogenetic package empowers scientists to study SARS-CoV-2 evolution and transmission at unprecedented scale and speed.
  • Enabled real-time analysis of viral evolution and transmission dynamics during the COVID-19 pandemic.
  • Facilitated global collaboration in understanding SARS-CoV-2 spread and adaptation.