README.md

Anopheles funestus introgression

Collection of scripts used for analyses and assembly of An. funestus complex data. Not everything is documented yet, but most scripts have some helpful information if you type python script.py -h.

Contents

• Manipulating FASTA files
• Parsing and calculating introgression statistics
• Calculating statistics for comparative genome assembly
• Misc population genetics scripts
• Calculating statistics from phylogenetic trees
• Manipulating, parsing, formatting, statistics from VCF files

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Manipulating FASTA files

Playing with fasta

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Parsing and calculating introgression statistics

Calculating introgression

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Calculating statistics for comparative genome assembly

Building and evaluating genomes

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Misc population genetics scripts

Some population genetics scripts

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Calculating statistics from phylogenetic trees

Traversing trees

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Manipulating, parsing, formatting, statistics from VCF files

Some things VCF