Scripts

• rename_fasta
  • Rename Mapping File Syntax
• beast_checkpoint
  • Example
  • Tracer
  • LogCombiner
• beast_wrapper
  • Example
• group_references
• degen
  • How-to
  • Example:
  • Output:
  • Gene/Tab File
  • Genbank File
• parallel_blast
  • Usage
  • Running inside of a PBS or SGE Job
• degen_regions
  • Usage
  • Using Genbank Files
  • Fetching Genbank Files Automatically
  • Using tab/csv file of gene annotation info
  • Manually specify CDS
  • Without Gene Information
  • Output
• plot_muts
  • Usage
  • Example comparing multiple sequences against a query sequence
  • Example using cluster method to use two references as x and y axis
  • Generating html graphics that are interactive
• fasta
  • Usage
  • Examples