Lecture

Phylogenetic Tree Construction

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In course

BIO-109: Introduction to life sciences (for IC)

Ce cours présente les principes fondamentaux à l'œuvre dans les organismes vivants. Autant que possible, l'accent est mis sur les contributions de l'Informatique aux progrès des Sciences de la Vie. ...

Description

This lecture covers the stages of building a phylogenetic tree using DNA sequences, starting with a distance matrix calculation and progressing through the UPGMA method. The process involves combining sequences with the fewest differences, calculating mean distances, and iteratively joining clades to construct the tree.

Instructor

Romain Zufferey

Teaching & PhD Courses Biology for engineers MSE-212 This course consists of an introduction to biology and more particularly to biology as a multidisciplinary field, emphasizing natural examples of materials engineering. It should therefore allow engineering students to find inspiration from biology in future materials research problems. Cellular biology and biochemistry for engineers BIO-105 Basic course in biochemistry as well as cellular and molecular biology for non-life

Official source

Ontological neighbourhood

Biology

Zoology: Topics in zoology

Related concepts (26)

Molecular phylogenetics

Molecular phylogenetics (məˈlɛkjᵿlər_ˌfaɪloʊdʒəˈnɛtɪks,_mɒ-,_moʊ-) is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree.

Computational phylogenetics

Computational phylogenetics is the application of computational algorithms, methods, and programs to phylogenetic analyses. The goal is to assemble a phylogenetic tree representing a hypothesis about the evolutionary ancestry of a set of genes, species, or other taxa. For example, these techniques have been used to explore the family tree of hominid species and the relationships between specific genes shared by many types of organisms.

Phylogenetics

In biology, phylogenetics (ˌfaɪloʊdʒəˈnɛtɪks,_-lə-) is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.

Phylogenetic nomenclature

Phylogenetic nomenclature is a method of nomenclature for taxa in biology that uses phylogenetic definitions for taxon names as explained below. This contrasts with the traditional approach, in which taxon names are defined by a type, which can be a specimen or a taxon of lower rank, and a description in words. Phylogenetic nomenclature is currently regulated by the International Code of Phylogenetic Nomenclature (PhyloCode). Phylogenetic nomenclature ties names to clades, groups consisting of an ancestor and all its descendants.

Phylogenetic comparative methods

Phylogenetic comparative methods (PCMs) use information on the historical relationships of lineages (phylogenies) to test evolutionary hypotheses. The comparative method has a long history in evolutionary biology; indeed, Charles Darwin used differences and similarities between species as a major source of evidence in The Origin of Species. However, the fact that closely related lineages share many traits and trait combinations as a result of the process of descent with modification means that lineages are not independent.

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Constructing Phylogenetic Trees: UPGMA Algorithm

Covers the UPGMA algorithm for constructing phylogenetic trees and understanding genetic relationships.

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Explores molecular evidence and mechanisms of evolution, including phylogenetic trees and protein comparisons.

Understanding Generative Models of Protein Sequences

Explores a unified framework for understanding and evaluating generative sequence models of DNA/RNA or Protein, covering topics like coevolution, conservation, and different models such as GREMLIN and BERT.

Exploring Evolution: Molecular Insights and Protein Comparison

Explores evolution through enzymes, DNA models, and protein comparisons, discussing molecular insights and evolutionary mechanisms.

Natural Selection and Species Origin