Journal: Journal of Molecular Evolution
Article title: Re-evaluating Adaptive Evolution of DRD4 in Aquatic Mammals: Taxon-Sampling Sensitivity of a Manatee Lineage Signal
Author: Yumi Shimozato
Affiliation: Ritsumeikan University, Research Organization of Science and Technology, Kusatsu, Japan
Corresponding author: Yumi Shimozato
Corresponding-author e-mail: umi.shimozato@gmail.com
Manuscript citation: Online Resource 2

Supplementary Code Archive
This archive contains the analysis scripts and workflow files developed and used for the reported DRD4 analyses. The code covers input preparation, branch-definition and topology preparation, HyPhy analysis execution, aggregation of saved results, robustness/sensitivity analyses, and preparation of manuscript-facing outputs.

Contents
- code/scripts/    Python analysis, preparation, aggregation, and finalization scripts.
- code/workflows/  GitHub Actions workflow files used for the documented analysis pipeline.
- software_versions.txt  Software versions and execution environment recorded for the analyses.

Public sequence accession numbers, sequence sources, and quality-control information are provided in Supplementary Table S1 (Online Resource 1). Numerical results used in the manuscript are reported in Supplementary Tables S2-S6 (Online Resource 1). Full run logs, intermediate analytical outputs, provenance manifests, and checksums are not included in this publication-facing code archive.
