dartR

dartR analyzes single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of amplified sequence tags) to perform data quality control, marker selection, and downstream population genetic analyses for conservation, ecology, and agriculture.

Key Features:

• SNP and Dominant Marker Handling: Analyzes single nucleotide polymorphisms (SNPs) and dominant markers such as presence/absence of amplified sequence tags.
• Data Quality Control and Marker Selection: Provides functions for data quality control and marker selection.
• Import/Export and Interoperability: Includes functions for importing, exporting, and linking data to facilitate integration with other bioinformatics packages.
• Simulation Functions: Contains simulation functions to generate datasets that can be analyzed within dartR.
• Expanded Functionality (Version 2): Version 2 increased the number of available functions from 45 to 144 to expand analytical capabilities for data manipulation and reporting.
• Performance Optimizations: Implements optimizations to improve function execution speed.

Scientific Applications:

• Conservation Biology: Analyzes genetic data to inform biodiversity management and species preservation decisions.
• Ecology: Supports studies of population genetics, gene flow, and evolutionary dynamics within ecosystems.
• Agriculture: Assists genetic analyses for crop and livestock breeding programs and genetic improvement strategies.

Methodology:

Functions explicitly include importing, exporting, and linking data; data quality control; marker selection; simulation of datasets; and analysis of SNPs and presence/absence amplified sequence tags, with performance optimizations for faster execution.