Phylo

A package for creating and manipulating phylogenies

Phylo is a Julia package that provides functionality for generating phylogenetic trees. It plays well with the Diversity package, i.e. to calculate phylogenetic diversity. Both are currently under development, so please raise an issue if you find any problems.

This package is currently less featured than the best phylogenetics packages in R or Python. Contributors are very welcome!

• Phylo.API
• • Usage
• Function list
• Phylo
• • A package for creating and manipulating phylogenies
• Getting tree attributes
• • Methods on TreeSets
  • Methods on Trees
  • Methods on Nodes
  • Methods on Branches
• Creating phylogenies
• • Reading phylogenies from disk
  • Writing phylogenies to disk
  • Creating random phylogenies
  • Importing phylogenies from R
• Building and manipulating trees
• Modelling traits on trees
• Plotting phylogenetic trees
• • Keywords
  • Example plots
  • Sorting trees for plotting
  • Coloring branches or nodes by a variable
• Routes along the tree
• Traversing and iterating over trees
• Modules and data types
• • Modules
  • Tree sets
  • Tree types
  • Node and Branch types
  • Iterator types
• Tutorial