Inferring demographic history and effective migration genome-wide in species pairs across Drosophila.
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Sample Metdata: Random selection (if possible) of publically-available sequences to use from NCBI. This contains filtering of metadata to ensure only WGS datasets containing a single individual were used, as well as data that
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Genome annotation via BRAKER2 with D. melangoaster proteins.
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Read filtering, mapping and variant calling for all pairs.
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Preprocessing of vcfs.
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Summary statistic calculation (coverage, hetA, hetB, hetAB, absolute genetic divergence).
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Filtering intronic intervals using BEDTOOLS.
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Extraction of distribution of pairwise divergence.
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Modelling via Mathematica notebooks.
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Analysis of modelling results in R.