API reference

The public API is small and kept stable. Import everything from the top level as usual (import forestpd as fpd); the pages below document each name where users import it from. Everything not listed here (forestpd.core, forestpd.cluster, forestpd.algo, and the rest of forestpd.io and forestpd.maf) is internal.

Where to find what

Names	Page
MaxMPDInstance, MaxMPDResult, MaxMPDStructure	Instances and results
optimize_maxmpd, optimize_many_maxmpd, evaluate_maxmpd	One-call functions
utils.prune, utils.split_system	Utilities
io.to_newick, io.to_splits_nexus, io.pz.from_phylozoo, io.pz.to_phylozoo	Input and output
maf.HeuristicMAF, maf.TieredMAF, maf.MaffeRMAF, maf.MaffeUMAF, maf.MAFComputer, maf.Rooting, maf.Forest	Agreement forests
PhyloTree, TaxonRegistry	Trees and taxa
ForestPDError and its subclasses, ForestPDWarning	Exceptions and warnings

Modules

• Instances and results
  • MaxMPDInstance
  • MaxMPDResult
  • MaxMPDStructure
• One-call functions
  • optimize_maxmpd()
  • optimize_many_maxmpd()
  • evaluate_maxmpd()
• Utilities
  • prune()
  • split_system()
• Input and output
  • to_newick()
  • to_splits_nexus()
  • PhyloZoo
• Agreement forests
  • Built-in stages
  • Writing your own stage
• Trees and taxa
  • PhyloTree
  • TaxonRegistry
• Exceptions and warnings
  • ForestPDError
  • ForestPDValueError
  • ForestPDInputError
  • ForestPDImportError
  • ForestPDWarning