VESPA

VESPA performs large-scale molecular evolutionary and selective pressure analyses of protein-coding sequences by automating gene-family identification, sequence alignment, phylogenetic reconstruction, and integration with codeML.

Key Features:

• Automation of preparatory steps: Identifies gene families, generates sequence alignments, and reconstructs phylogenetic trees for large datasets.
• Selective pressure analysis: Integrates with codeML to perform selective pressure inference and assess variation in selective pressures across gene families and species.
• Result interpretation and summarization: Parses codeML outputs and generates simplified summary files of selective pressure results.
• Implementation and scalability: Implemented in Python and tailored for UNIX environments to handle large genomic datasets.

Scientific Applications:

• Large-scale molecular evolution: Analysis of protein-coding sequence evolution across extensive multi-species datasets.
• Selective pressure comparison: Detection and comparison of selective pressures across gene families and species using codeML.
• Gene-family and phylogenetic studies: Reconstruction of phylogenies and study of gene-family evolutionary dynamics across numerous species.

Methodology:

Automated gene-family identification, sequence alignment, phylogenetic tree reconstruction, integration with codeML for selective pressure analyses, and automatic parsing and summarization of codeML results; implemented in Python for UNIX.