nQuack

nQuack estimates ploidal level from sequence data using site-based heterozygosity and Gaussian Mixture Models to address statistical shortcomings in existing methods.

Key Features:

• Model Selection: nQuack performs model selection for improved ploidy predictions using expected maximization algorithms.
• Distribution Options: Implements expected maximization algorithms with normal, beta, and beta-binomial distributions.
• Simulation Validation: Validated using extensive computer simulations that account for variability in sequencing depth, as well as real data sets.

Scientific Applications:

• Ploidy Prediction: Predicts ploidal level from DNA sequence data based on site-based heterozygosity.
• Cytotype Estimation: Provides an alternative to traditional tedious methods of ploidal level estimation by leveraging sequence data.

Methodology:

nQuack uses expected maximization algorithms with normal, beta, and beta-binomial distributions, and employs Gaussian Mixture Models for model selection in ploidy prediction.