POPBAM

POPBAM performs evolutionary analyses of whole-genome alignments across multiple individuals, populations, or species by directly operating on BAM-formatted sequencing alignments to call variants and compute population-genetic statistics.

Key Features:

• Direct BAM File Processing: Operates directly on BAM-formatted assembly files from next-generation sequencing alignments.
• Variant Site Calling: Identifies variant sites within genomic alignments.
• Evolutionary Sequence Statistics: Calculates nucleotide diversity, population divergence, linkage disequilibrium, and mutation frequency spectra across two or more populations.
• Sliding Window Analysis: Performs analyses in sliding windows along chromosomes or scaffolds.
• Phylogenetic Tree Construction: Generates phylogenetic trees from samples contained in a BAM file.
• Implementation and Performance: Implemented in C/C++ to provide fast processing, memory efficiency, and scalability for large datasets.

Scientific Applications:

• Population Genomics: Enables genome-wide analyses of genetic diversity and population divergence across many individuals and populations.
• Detection of Selection and Mutation Effects: Supports investigation of natural selection and mutation effects on phenotypes via sequence statistics and frequency spectra.
• Speciation and Phylogeography: Facilitates studies of speciation processes and evolutionary relationships through phylogenetic tree construction.
• Genome-wide Scans: Suitable for comprehensive sliding-window scans for diversity, divergence, and linkage patterns across chromosomes or scaffolds.

Methodology:

Processes BAM-formatted assembly files to call variant sites, computes nucleotide diversity, population divergence, linkage disequilibrium, and mutation frequency spectra across populations, performs sliding-window analyses along chromosomes or scaffolds, and constructs phylogenetic trees; implemented in C/C++ for performance and memory efficiency.