Methods Mol Biol. 2026;2983:397-447. doi: 10.1007/978-1-0716-4901-5_32.
ABSTRACT
Nucleotide sequence analyses provide insights into changes that might have an impact on proteins and their function. With the rapid accumulation of sequence data, it is now possible to recover the evolutionary history of most genes at the population level to species and beyond. Those sequences can be compared for substitutions that might change or not change the encoded protein and its function, but they can also help to estimate evolutionary relationships. These hypotheses, as phylogenetic trees, provide visual and statistical guidance for characterizing the degree of relatedness among biological entities. In a phylogenetic tree, ancestor-descendant relationships are represented by connections, and closely related entities share most of these links, which represent their evolutionary closeness. In this chapter, I outlined a method to retrieve and label nucleotide sequences of the cytokine IL17A gene, align them to identify substitutions in homologous sites, estimate phylogenetic trees with support values, and visualize these trees as images. The methodology outlined here uses free software packages in the R environment and the Python language.
PMID:41478993 | DOI:10.1007/978-1-0716-4901-5_32
