- App
- CharactersBlock
- CharactersBlockBuilder
- CharactersBlockListener
- CharactersBlockParser
- DataBlock
- DataBlockBuilder
- DataBlockListener
- DataBlockParser
- DistanceBasedTreeMethod
- DistancesBlock
- DistancesBlockBuilder
- DistancesBlockListener
- DistancesBlockParser
- MultipleHitCorrection
- NexusBlock
- NexusBlock.Abstract
- NexusBlockBuilder
- NexusBlockBuilder.Abstract
- NexusBlockListener
- NexusBlockParser
- NexusBlockParser.Abstract
- NexusComment
- NexusFile
- NexusFileBuilder
- NexusFileFormat
- NexusFileListener
- NexusFileListener.Abstract
- NexusObject
- ParsimonyTreeMethod
- PHYLIPFileBuilder
- PHYLIPFileFormat
- PHYLIPFileListener
- TaxaBlock
- TaxaBlockBuilder
- TaxaBlockListener
- TaxaBlockParser
- TreesBlock
- TreesBlock.NewickTreeString
- TreesBlockBuilder
- TreesBlockListener
- TreesBlockParser