This GitHub page accompanies a manuscript currently under review.
There are additional scripts available that detail other analyses performed that didn't make it into the final analyses, however the most relevant scripts to look at (as it pertains to the manuscript) are:
Markdown/Figure_1_internal_tree_w_refseq_refs.Rmd
Markdown/Figures_2_4_5_internal_only.Rmd
Markdown/SKA_analysis_100_SNPs.Rmd
Markdown/QC_workflow.Rmd
Genomic data is in results
, metadata and other info is in delims
, QC data is in QC_summaries
and bacsort
contains files used in the running of BacSort for phylogenetic assignment