appl: tranalign [
  documentation: "Align nucleic coding regions given the aligned proteins"
  groups: "Alignment:Multiple"
]

section: input [ info: "input Section" type: page ]

seqall: nsequence  [
  parameter: "Y"
  type: "nucleotide"
  info: "Nucleotide sequences to be aligned"
]

seqset: psequence  [
  parameter: "Y"
  type: "gapprotein"
  info: "Protein sequence alignment"
]

endsection: input

section: advanced [ info: "advanced Section" type: page ]

list: table  [
  optional: "Y"
  default: "0"
  minimum: "1"
  maximum: "1"
  header: "Genetic codes"
  values: "0:Standard; 1:Standard (with alternative initiation codons); 2:Vertebrate Mitochondrial; 3:Yeast Mitochondrial; 4:Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma; 5:Invertebrate Mitochondrial; 6:Ciliate Macronuclear and Dasycladacean; 9:Echinoderm Mitochondrial; 10:Euplotid Nuclear; 11:Bacterial; 12:Alternative Yeast Nuclear; 13:Ascidian Mitochondrial; 14:Flatworm Mitochondrial; 15:Blepharisma Macronuclear; 16:Chlorophycean Mitochondrial; 21:Trematode Mitochondrial; 22:Scenedesmus obliquus; 23:Thraustochytrium Mitochondrial"
  delimiter: ";"
  codedelimiter: ":"
  prompt: "Code to use"
]

endsection: advanced

section: output [ info: "output Section" type: page ]

seqoutset: outseq  [
  parameter: "Y"
]

endsection: output
