ALPHA

ALPHA infers local genealogies across genomic alignments to characterize region-specific evolutionary histories and to detect processes such as recombination and introgression.

Key Features:

• Automated inference: Automated inference of local genealogies across genomic alignments.
• Sliding window approach: Construction of local genealogies using a sliding window technique to analyze discrete regions within alignments.
• Comprehensive statistical analysis: Computation of statistics derived from local phylogenies, including the D-statistic for detecting introgression.
• Import/export integration: Support for import and export of alignment and genealogy data to integrate with other bioinformatics workflows.

Scientific Applications:

• Species phylogeny: Enhancing resolution of species trees by incorporating local genealogical variation.
• Evolutionary processes: Investigating fine-scale mechanisms such as recombination, selection, and introgression.
• Trait mapping: Associating specific genomic regions with phenotypic traits through local phylogenetic analysis.

Methodology:

Construction of local genealogies using a sliding window approach, automated inference across genomic alignments, and computation of local-phylogeny statistics including the D-statistic.