BABAPPA: An Automated Pipeline for Codeml Mediated Selection Analysis Integrating PRANK and IQ-TREE2

Abstract

Episodic selection analyses are often assembled from fragmented toolchains in which ortholog discovery, codon alignment, phylogeny, exploratory scans, branch-site testing, and reporting are handled separately, making reproducibility and sensitivity tracking difficult. We introduce BABAPPASnake as an integrated workflow contribution for orthogroup-centered episodic selection analysis. The workflow combines orthogroup construction logic, CDS quality-aware mapping, multi-engine alignment pathways, phylogenetic inference, exploratory nomination, and branch-site follow-up testing in one reproducible execution framework. It also supports optional HyPhy GARD recombination screening as a conservative preprocessing report layer without forcing fragment-level rerouting by default. It generates pathway-level and cross-pathway robustness outputs, including matrix, consensus, narrative, and provenance summaries to support sensitivity-aware interpretation. A four-gene mosquito melanization-associated module is analyzed as a real-data empirical demonstration of end-to-end workflow behavior. In this demonstration, branch/site signals show both recurrent and method-sensitive components across six method-trim pathways, with a directional core-tier tendency in several summaries. These case-study patterns are interpreted as workflow-based empirical evidence and hypothesis-generating asymmetry, not decisive pathway-level confirmation. Overall, BABAPPASnake provides a practical and reproducible framework for episodic selection studies where analytical sensitivity must be explicitly reported.