An alignment of discrete character states, where states are integers.

Methods

  • ages
    • gets the ages of these taxa as an array of doubles.
  • canonicalStateCount
    • the number of canonical states excluding ambiguous states in the alignment.
  • canonicalStates
    • the canonical states excluding ambiguous states.
  • dataType
    • get the data type of this alignment.
  • length
    • gets the number of taxa.
  • nchar
    • The number of characters/sites.
  • nodeCount
    • the total number of nodes (left + internal) in a binary tree with these taxa.
  • species
    • gets the species of these taxa as an array of strings.
  • stateCount
    • the number of possible states including ambiguous states in the alignment.
  • states
    • the possible states including ambiguous states.
  • taxa
    • the taxa of the alignment.
  • taxaNames
    • The names of the taxa.

      Examples

  • simpleSerialCoalescentNex.lphy
  • twoPartitionCoalescentNex.lphy