LMAP

LMAP performs high-throughput multigene analyses using PAML's codeml to evaluate codon substitution models and detect adaptive evolution in protein-coding sequences.

Key Features:

• Comprehensive Model Support: Supports all codon substitution models available in codeml, including site models, branch models, branch-site models, and clade models.
• Automated codeml Workflow: Automates directory organization, execution, and results gathering and organization for Likelihood Ratio Test estimations.
• High-Throughput Multi-core Processing: Designed for workstation multi-core environments to process multiple datasets simultaneously and scale to more than 20 concurrent datasets.
• Minimal Input Requirements: Requires a multiple sequence alignment file and a phylogenetic tree file in a single input directory.
• Implementation: Implemented in Perl.
• Pipeline Integration: Can be integrated into larger bioinformatics pipelines for multigene comparative analyses.

Scientific Applications:

• Detection of Positive Selection: Identifying genes or sites under positive selection using codon substitution models and Likelihood Ratio Tests.
• Comparative Genomics: High-throughput analysis of multiple genes or datasets derived from genome sequencing projects to study adaptive evolution and phenotypic diversity.
• Phylogenetic Hypothesis Testing: Testing site-, branch-, branch-site-, and clade-specific selection hypotheses across phylogenies.

Methodology:

Automates the codeml workflow from directory organization and execution to results gathering and organization for Likelihood Ratio Test estimations; uses PAML codeml with site, branch, branch-site, and clade codon substitution models, is implemented in Perl, and is optimized for workstation multi-core processing of multiple datasets.