BABAPPAlign

BABAPPAlign Zenodo Package collects the files required for manuscript review, software inspection, and practical reproducibility of the revised BABAPPAlign submission. The archive includes the BABAPPAlign source code and packaging files, installation and usage documentation, tests, example input files, final manuscript and supplementary materials, figure-generation scripts, reviewer-response documents, deterministic benchmark manifests, external validation manifests, benchmark archives used in the revised evaluation, and manuscript-facing result tables and figures. This deposit is organized to support transparent evaluation of the revised benchmarking framework. Included materials allow inspection of the software, examination of the manuscript package, and reproduction of the reviewer-focused analyses using the supplied manifests and scripts. Final outputs used in the manuscript are already included under the results directory for direct verification. Large local caches, virtual environments, benchmark logs, and bulky intermediate alignment directories are intentionally excluded. Pretrained BABAPPAScore model weights are distributed separately via Zenodo, and the software archive DOI and model DOI are documented within the package metadata. Integrity verification files and citation metadata are also included.