ADOPS

ADOPS detects positively selected amino acid sites from unaligned nucleotide sequence data to infer adaptive evolution using codon substitution models and phylogenetic analysis.

Key Features:

• Alignment-free analysis: Directly analyzes unaligned nucleotide sequence data without requiring pre-alignment.
• Maximum-likelihood codon models: Employs maximum-likelihood methods based on codon substitution models to estimate selection at specific sites.
• Integrated phylogenetic inference: Automatically constructs phylogenetic trees to contextualize evolutionary relationships during selection analysis.
• Site-level output: Identifies amino acid sites under positive selection and provides site-specific results for downstream biological interpretation.

Scientific Applications:

• Evolutionary biology: Detection of adaptive changes in protein-coding genes across taxa.
• Molecular genetics: Identification of amino acid sites under selection for studies of gene and protein function.
• Case study application: Applied to analyze 54 Coffea putative S-RNase sequences to identify adaptive changes.

Methodology:

Accepts unaligned nucleotide sequence data; applies codon substitution models within a maximum-likelihood framework to estimate positive selection at sites; automatically infers phylogenetic trees; and identifies amino acid sites under positive selection.