Phyloscanner Manual

• I Inferring within- and between-host phylogenies in windows along the genome, using mapped reads
  • The basic command
    • The Python version you use
  • What do the window coordinates mean exactly?
  • What windows should I choose?
    • Start & end
    • Window width
    • Window overlap
  • What output files are produced?
  • Optional arguments
    • Window options
    • Recommended options
    • Read quality options
    • Other assorted options
    • Options for bioinformatic interrogation
    • Partial processing options
    • Deprecated options
• II Analysing within- and between-host phylogenies
  • The basic command
  • Name format for input files
  • Output
  • Preparing the trees
  • Tip label and file suffix regular expressions
  • Branch length normalisation
    • Parallelising tools/CalculateTreeSizeInGenomeWindows.py
  • Blacklisting
    • Duplicate blacklisting
    • Parsimony-based blacklisting for contaminants
    • Dual infection blacklisting
    • User blacklisting
    • Downsampling
    • Pruning the blacklist
  • Parsimony reconstruction
  • Summary statistics
  • Classification of pairwise relationships
  • Pairwise relationship summary
  • Miscellaneous options