LMAP_S

LMAP_S performs high-throughput multiple sequence alignment (MSA) and phylogenetic tree (PT) estimation for multigene evolutionary analyses.

Key Features:

• High-Throughput Capability: Supports processing of more than 20 datasets simultaneously for large-scale analyses.
• Comprehensive Workflow Automation: Automates MSF preparation, MSA estimation, outlier detection, alignment refinement, consensus building, phylogeny estimation, phylogeny comparison, and editing while managing file and directory organization and execution.
• Integration of Multiple Software: Integrates over 25 scientific software packages and offers more than 65 algorithm choices distributed across five stages of analysis.
• Optimal Estimation Focus: Targets optimal estimations of both MSAs and phylogenies to support studies of phenotypic diversity and adaptive evolution in protein-coding genes.
• Multi-Core Environment Optimization: Designed for workstation multi-core environments to leverage parallel processing capabilities.
• Additional Application — RYcode.pl: Includes RYcode.pl for purine/pyrimidine DNA/RNA (re-)coding.

Scientific Applications:

• Evolutionary Biology: Enables analysis of phenotypic diversity and adaptive evolution in protein-coding genes through combined MSA and phylogeny estimation.
• Comparative Genomics and Multigene Phylogenetics: Supports multigene alignment and phylogenetic inference across gene families for comparative studies.
• Large-Scale Genomic Data Analysis: Facilitates handling and analysis of extensive genomic datasets in high-throughput workflows.

Methodology:

Automated workflow performing MSF preparation, MSA estimation, outlier detection, alignment refinement, consensus building, phylogeny estimation, phylogeny comparison and editing, integrated execution and file/directory management using multiple software packages and algorithm choices, and optimized for multi-core workstation environments.