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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...
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...
Evolution of Microbial Genome01:08

Evolution of Microbial Genome

Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.
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...
Eukaryotic Evolution01:24

Eukaryotic Evolution

The endosymbiont theory is the most widely accepted theory of eukaryotic evolution; however, its progression is still somewhat debated. According to the nucleus-first hypothesis, the ancestral prokaryote first evolved a membrane to enclose DNA and form the nucleus. Conversely, the mitochondria-first hypothesis suggests that the nucleus was formed after endosymbiosis of mitochondria.
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...

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A Practical Guide to Phylogenetics for Nonexperts
12:00

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Published on: February 5, 2014

Ancestors 1.0: a web server for ancestral sequence reconstruction.

Abdoulaye Banire Diallo1, Vladimir Makarenkov, Mathieu Blanchette

  • 1Department of Computer Science, Université du Québec à Montréal, PO. Box 8888 Downtown Station, Montreal, QC H3C3P8, Canada. diallo.abdoulaye@uqam.ca

Bioinformatics (Oxford, England)
|October 24, 2009
PubMed
Summary

Ancestors 1.0 simplifies ancestral genome reconstruction by integrating sequence alignment, indel history, and substitution inference. This web server provides posterior probabilities and error rates for accurate ancestral base predictions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Ancestral genome reconstruction involves complex computational steps.
  • Existing frameworks lack integration for these steps.
  • Ancestors 1.0 addresses the need for a unified workflow.

Purpose of the Study:

  • To introduce Ancestors 1.0, a web server for ancestral genome reconstruction.
  • To provide an integrated and user-friendly workflow for key reconstruction steps.

Main Methods:

  • Implements multiple sequence alignment algorithms.
  • Utilizes a maximum likelihood solver for indel history reconstruction.
  • Employs a context-dependent maximum likelihood algorithm for substitution inference.

Main Results:

  • Provides posterior probabilities for ancestral genome reconstruction steps.
  • Calculates the expected error rate for each ancestral base prediction.
  • Offers an integrated approach for the final three steps of reconstruction.

Conclusions:

  • Ancestors 1.0 facilitates efficient and accurate ancestral genome reconstruction.
  • The server integrates essential computational steps into an accessible workflow.
  • Results include valuable metrics for assessing the reliability of predictions.