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1. mcorr mcorr Public

   Inferring bacterial recombination rates from large-scale sequencing datasets.

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2. viral-mcorr viral-mcorr Public

   Using correlated substitutions to infer recombination rates in RNA viruses

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3. ReferenceAlignmentGenerator ReferenceAlignmentGenerator Public

   Mapping reads to the reference genome to construct consensus genomes and generate alignments

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4. popsimu popsimu Public

   A GO package for population simulation with horizontal gene transfer

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5. hgtlib hgtlib Public

   forward population simulations with selection and recombination

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6. PangenomeAlignmentGenerator PangenomeAlignmentGenerator Public

   Align SRAs to pangenome FASTA file generated by Roary

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