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1. Dendrogram Dendrogram Public

   This is a dendrogram R Script using Structural protein phylogeny information and amino acid phylogeny information.

2. Species-and-Subspecies-from-MASH Species-and-Subspecies-from-MASH Public

   This code is taking MASH output and sorting fasta files into folders for species and subspecies determination and frequency. At the end of the code visualizations and executed for viewing of outputs.

3. Phylo-tree- Phylo-tree- Public

   Python

4. DissimilarTrees DissimilarTrees Public

   Building an ANI Based Phylogenetic Tree

   Python

5. mab-dcc-pipeline mab-dcc-pipeline Public

   Snakemake pipeline for assigning M. abscessus clinical isolates to Dominant Circulating Clones (DCC1–7) and identifying transmission pairs from whole genome sequencing data

   Python

6. MAbsIslandScanner MAbsIslandScanner Public

   MAbsIslandScanner: A genomic island detection tool calibrated for Mycobacteroides abscessus clinical genomics

   Python