An alignment containing metadata and parsed from a nexus file.

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.
  • charset
    • return a partition alignment. If the string doesn’t match charset’s syntax, then check if the string matches a defined name in the nexus file. Otherwise it is an error. The string is referred to one partition at a call, but can be multiple blocks, such as a dummy example: d.charset([“2-457\3”, “660-896\3”, “1-.\3”]).
  • charsets
    • return an alignment array defined by charsets, which could be pre-defined in the nexus file.
  • dataType
    • get the data type of this alignment.
  • getTaxaNames
    • The names of the taxa.
  • 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

  • twoPartitionCoalescentNex.lphy
  • https://linguaphylo.github.io/tutorials/time-stamped-data/