Beyond mutations: accounting for selection and self-organization in the analysis of protein evolution

Molecular phylogenetic research has relied on the analysis of the coding sequences by genes or of the amino acid sequences by the encoded proteins. Enumerating the numbers of mismatches, being indicators of mutation, has been central to pertinent algorithms. However, the constraining forces of selection and self-organization have been unaccounted for in conventional approaches, possibly causing available models to fall short of representing the actual evolutionary history. Specific amino acids possess quantifiable characteristics that enable the conversion from “words” (strings of letters denoting amino acids or bases) to “waves” (strings of quantitative values representing the physico-chemical properties) or to matrices (coordinates representing the positions in a comprehensive property space). The application of such numerical representations to evolutionary analysis takes into account not only mutation but also selection/self-organization as influences that drive speciation, because ..., , , # Beyond Mutations: Accounting for Selection and Self-Organization in the Analysis of Protein Evolution

[https://doi.org/10.5061/dryad.tht76hf63](https://doi.org/10.5061/dryad.tht76hf63)

## Description of the data and file structure

Publicly accessible sequences were collected from the NCBI landmark model organisms and then sought to add representatives of diverse clades from NCBI nucleotide.

## Sharing/Access information

Data was derived from the following sources:

* NCBI

## Code/Software

NA