bpositive

bpositive enables analysis of positive selection in protein sequences to identify adaptive amino acid changes using ADOPS-compatible batch processing and centralized project storage.

Key Features:

• Integration with ADOPS: Extends the Adaptive Divergence Of Protein Sequences (ADOPS) framework and operates on ADOPS project files.
• Batch processing and scalability: Provides batch processing capabilities to analyze hundreds to thousands of sequence files or ADOPS projects.
• Centralized repository for ADOPS projects: Stores ADOPS projects and their results to enable management of large datasets.
• Support for maximum-likelihood codon models: Enables analyses based on codon substitution models, including codeml, to infer positive selection at amino acid sites.
• Repeatability and data reuse: Centralization of results promotes reproducibility and facilitates reuse of prepared datasets across analyses.

Scientific Applications:

• Detection of positive selection: Identification of amino acid sites under positive selection in protein-coding genes using maximum-likelihood codon substitution models.
• Comparative and large-scale evolutionary analyses: Support for genome-scale or multi-gene studies across diverse organisms by handling large numbers of ADOPS projects.

Methodology:

Collect sequence data and run ADOPS to infer positively selected amino acid sites using maximum-likelihood codon substitution models (e.g., codeml), with results managed in a centralized database to enable batch processing and large-dataset management.