application: ftreedist [
  documentation: "Distances between trees"
  groups: "Phylogeny:Consensus"
  embassy: "phylipnew"
]

section: input [
  information: "Input section"
  type: "page"
]

  tree: intreefile [
    parameter: "Y"
    knowntype: "newick"
    information: "Phylip tree file"
  ]

endsection: input

section: additional [
  information: "Additional section"
  type: "page"
]

  list: dtype [
    additional: "Y"
    information: "Distance type"
    values: "s:Symmetric difference; b:Branch score distance"
    default: "b"
  ]

  list: pairing [
    additional: "Y"
    information: "Tree pairing method"
    values: "a:Distances between adjacent pairs in tree file;
             p:Distances between all possible pairs in tree file"
    default: "a"
  ]

  list: style [
    additional: "Y"
    information: "Distances output option"
    values: "f:Full matrix; v:One pair per line, verbose; s:One pair
             per line, sparse"
    default: "v"
  ]

  boolean: noroot [
    additional: "Y"
    default: "N"
    information: "Trees to be treated as rooted"
  ]

  integer: outgrno [
    additional: "Y"
    minimum: "0"
    default: "0"
    information: "Species number to use as outgroup"
  ]

endsection: additional

section: output [
  information: "Output section"
  type: "page"
]

  outfile: outfile [
    parameter: "Y"
    knowntype: "treedist output"
    information: "Phylip treedist program output file"
  ]

  boolean: progress [
    additional: "Y"
    default: "Y"
    information: "Print indications of progress of run"
  ]

endsection: output
