Scripts and data sets associated with: On testing homogeneity of the evolutionary process using alignments of homologous sequences

In 2019, Genome Biology and Evolution (11:3341-3352) published three statistical tests for assessing whether alignments of genome sequences violate the phylogenetic assumption of evolution under homogeneous conditions. The new tests extend the matched-pairs tests of symmetry, marginal symmetry, and internal symmetry for alignments of n = 2 homologous sequences of nucleotides or amino acids to cases where alignments of n > 2 sequences are considered. Here we discuss the limitations of these new tests and then outline alternative approaches, which permit formal testing of multiple hypotheses (i.e., by controlling either the family-wise error rate or the false discovery rate). We show that the other approaches provide much greater insight into variation of the evolutionary process across lineages, via informal graphical methods and formal statistical procedures. Using one of the procedures (i.e., the Bonferroni test), we show that evolution under heterogeneous conditions is more prevale..., This submission contains batch scripts, sequence data, and protocols describing what was done in five computer-based experiments outlined in the manuscript with the above-mentioned title. The format of the submission was chosen such that it is as FAIR compliant as possible (i.e., that the data are Findable, Accessible, Interoperable, and Resuasable). In other words, the research done in the five experiment is reproducible.

The content in folder Experiment_1 relates to the analysis of the performance of the Maximum Symmetry test. In particular, the experiment was designed to ascertain whether the edge lengths of a tree have an impact on the Type I error rate. The file named 00_README, describe the method used.
The content in folder Experiment_2 relates to the analysis of the performance of the Maximum Symmetry test. In particular, the experiment was designed to ascertain whether the edge lengths of a tree have an impact on the Type II error rate. The file named 00_README, describe the m..., , # Scripts and data sets associated with \"On Testing Homogeneity of the Evolutionary Process using Alignments of Homologous Sequences\"

This DRYAD submission contains batch scripts, sequence data, and explanations of what was done in five computer-based experiments described in the manuscript with the above-mentioned title.

* The content in folder Experiment_1 relates to the analysis of the performance of the Maximum Symmetry test. In particular, the experiment was designed to ascertain whether the edge lengths of a tree have an impact on the Type I error rate.
* The content in folder Experiment_2 relates to the analysis of the performance of the Maximum Symmetry test. In particular, the experiment was designed to ascertain whether the edge lengths of a tree have an impact on the Type II error rate.
* The content in folder Experiment_3 relates to the analysis of the performance of the Maximum Symmetry test. In particular, the experiment was designed to ascertain whether alignmen...