PoPoolation

PoPoolation computes population genetic parameters from pooled sequence data to estimate genetic diversity and detect selection across genomes.

Key Features:

• Population Genetic Parameter Estimation: Calculates θ (Watterson), θ (π), and Tajima's D from pooled sequence data.
• Bias Correction: Implements corrections for biases introduced by pooling samples and sequencing errors.
• Species Divergence Consideration: Accounts for divergence between species when analyzing sequence data.
• Graphical Display: Generates sliding-window plots for genome-wide visualization of genetic variation.
• Programming Languages and Data Formats: Implemented in Perl and R and supports commonly used data formats.
• Evaluation of Influencing Factors: Evaluates impacts of mapping algorithms, sequencing errors, and read coverage on the accuracy of parameter estimates from pooled data.

Scientific Applications:

• Evolutionary Biology: Enables analysis of genetic diversity and tests for selection in evolutionary studies.
• Conservation Genetics: Supports genome-wide assessment of genetic variation relevant to conservation genetics.
• Population Genomic Surveys: Facilitates genome-wide analyses of population structure and adaptive evolution using pooled samples.

Methodology:

Computes θ (Watterson), θ (π), and Tajima's D; applies bias correction for pooling and sequencing errors; accounts for species divergence; performs sliding-window genome-wide analyses; and evaluates effects of mapping algorithms, sequencing errors, and read coverage.