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Phylogenetic Analyses of Chemokine Receptors from Sequence Retrieval to Phylogenetic Trees

  • Juan C. SantosEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2108)

Abstract

Phylogenetic trees are an essential requisite for comparative biology studies where hypotheses regarding the evolution of genes can be investigated. Trees provide visual and statistical guides to characterize the degree of relatedness among biological entities from genes to species. In a tree, ancestor-descendant relationships are represented by connections, and closely related entities share most of these links. In this chapter, I outlined a method to retrieve and label amino acid and nucleotide sequences of chemokine receptors, align them in sequence matrices, determine their best-model of molecular evolution, and estimate the corresponding phylogenetic trees with distance and maximum likelihood approaches. Most of these analyses are performed within the R environment, and all of these methods use open-source software.

Key words

Amino acids Nucleotides Automatic sequence retrieval Alignment Homology Substitution models Maximum likelihood Neighbor joining Phylogenetic trees 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of Biological Sciences, College of Liberal Arts and SciencesSt. John’s UniversityQueensUSA

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