This chapter introduces distance-based tree-building methods. It begins with the calculation of pairwise genetic distances from aligned DNA sequences and shows how matrices are generated. The unweighted pair group method with arithmetic mean (UPGMA) is presented as a clustering algorithm that assumes a molecular clock, with limitations highlighted. To account for rate variation across lineages, the Fitch-Margoliash method is discussed. The neighbour-joining (NJ) method is introduced as a more flexible alternative that accommodates rate variation across lineages. Optimality criteria-based approaches, including minimum evolution and least squares, are explained as improvements over simple clustering, as they evaluate multiple topologies.

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Methods of Tree Building Using DNA Sequence Data-I: Distance Approach

  • K. Praveen Karanth

摘要

This chapter introduces distance-based tree-building methods. It begins with the calculation of pairwise genetic distances from aligned DNA sequences and shows how matrices are generated. The unweighted pair group method with arithmetic mean (UPGMA) is presented as a clustering algorithm that assumes a molecular clock, with limitations highlighted. To account for rate variation across lineages, the Fitch-Margoliash method is discussed. The neighbour-joining (NJ) method is introduced as a more flexible alternative that accommodates rate variation across lineages. Optimality criteria-based approaches, including minimum evolution and least squares, are explained as improvements over simple clustering, as they evaluate multiple topologies.