v0.4.0

• Introducing ripples
  • searches for possible recombinant nodes in a MAT using a phylogenetic approach
  • option to limit search to user-specified samples and their ancestors.
• New matOptimize
  • Handles ambiguities and stores Fitch states at each node
  • Faster and better parallelism
  • Exhaustive SPR search
• Several features added to matUtils
  • summary includes a new option --haplotype to collects the number of unique sets of mutations across the entire input tree
  • summary --clades refactored to produces both inclusive and exclusive sample counts
  • summary adds -E option to include contextual information including timespan parsing in RoHO
  • uncertainty includes a new option for identifying locally recurrent mutations
  • new items included in summary --aberrant
  • matUtils annotate includes a new option --clade-paths
• Several changes to improve code quality, including stylizing with ASytle