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1. ancestral reconstruction and likelihood analysis for CRISPR spacer arrays

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2. Goldfinder detects gene co-occurrence and avoidance accounting for phylogenetic relationships

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3. AIMsetfinder is a collection of Rscripts to identify sets of Ancestry Informative Markers (AIMs), that minimize the logloss error of a naive Bayes classifier.

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5. panicmage can estimate gene gain and loss rates, the size of pan-genomes, and test for neutral evolution.

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6. A coalescent theory based tool to identify oversampling in prokaryotic strain collections

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