AlexandrusPS

AlexandrusPS automates detection of orthologous gene clusters and conducts CodeML-based positive selection analyses on coding sequence and peptide datasets to study adaptive evolution.

Key Features:

• Orthology Prediction: Performs orthology prediction to identify homologous genes and establish gene family associations across species.
• CodeML Configuration Management: Prepares and organizes configuration files required for CodeML positive selection analyses.
• Positive Selection Analysis: Uses CodeML to compute maximum likelihood estimates and perform log-likelihood tests to detect positive selection at the codon level.
• Input Formats: Accepts coding sequence (CDS) and peptide FASTA files as input for downstream analyses.
• Transcriptome-wide Analysis: Enables selection analyses across large, transcriptome-scale gene sets.

Scientific Applications:

• Comparative Genomics: Identify genes under positive selection across multiple species to compare evolutionary trajectories.
• Molecular Evolution: Investigate selective pressures and adaptive evolution on protein-coding genes.
• Phylogenetics: Support analyses of evolutionary dynamics within and between gene families.
• Adaptation and Functional Inference: Reveal pathways and processes potentially involved in environmental or lineage-specific adaptation.

Methodology:

Accepts CDS and peptide FASTA inputs, performs orthology prediction, generates CodeML configuration files, and runs CodeML to obtain maximum likelihood estimates and perform log-likelihood tests for positive selection.