application: fdnacomp [
documentation: "DNA compatibility algorithm"
groups: "Phylogeny:Molecular sequence"
embassy: "phylipnew"
relations: "EDAM_topic:0084 Phylogenetics"
relations: "EDAM_operation:0547 Phylogenetic tree construction (maximum likelihood and Bayesian methods)"
]
section: input [
information: "Input section"
type: "page"
]
seqsetall: sequence [
parameter: "Y"
type: "gapdnaphylo"
aligned: "Y"
help: "File containing one or more sequence alignments"
relations: "EDAM_data:2887 Sequence record (nucleic acid)"
]
tree: intreefile [
parameter: "Y"
nullok: "Y"
knowntype: "newick"
information: "Phylip tree file (optional)"
relations: "EDAM_data:0872 Phylogenetic tree"
]
properties: weights [
standard: "Y"
information: "Phylip weights file (optional)"
length: "$(sequence.length)"
nullok: "Y"
knowntype: "weights"
relations: "EDAM_data:2994 Phylogenetic character weights"
]
endsection: input
section: additional [
information: "Additional section"
type: "page"
]
integer: outgrno [
additional: "Y"
minimum: "0"
default: "0"
maximum: "$(sequence.count)"
failrange: "N"
trueminimum: "Y"
information: "Species number to use as outgroup"
relations: "EDAM_data:2527 Parameter"
]
integer: njumble [
additional: "@(!$(intreefile.isdefined))"
information: "Number of times to randomise"
minimum: "0"
default: "0"
relations: "EDAM_data:2527 Parameter"
]
integer: seed [
additional: "$(njumble)"
information: "Random number seed between 1 and 32767 (must
be odd)"
minimum: "1"
maximum: "32767"
default: "1"
relations: "EDAM_data:2527 Parameter"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
outfile: outfile [
parameter: "Y"
knowntype: "dnacomp output"
information: "Phylip dnacomp program output file"
relations: "EDAM_data:0872 Phylogenetic tree"
]
toggle: trout [
additional: "Y"
default: "Y"
information: "Write out trees to tree file"
relations: "EDAM_data:2527 Parameter"
]
outfile: outtreefile [
additional: "$(trout)"
extension: "treefile"
information: "Phylip tree output file (optional)"
knowntype: "newick tree"
nullok: "Y"
relations: "EDAM_data:0872 Phylogenetic tree"
]
boolean: printdata [
additional: "Y"
default: "N"
information: "Print data at start of run"
relations: "EDAM_data:2527 Parameter"
]
boolean: progress [
additional: "Y"
default: "Y"
information: "Print indications of progress of run"
relations: "EDAM_data:2527 Parameter"
]
boolean: treeprint [
additional: "Y"
default: "Y"
information: "Print out tree"
relations: "EDAM_data:2527 Parameter"
]
boolean: stepbox [
additional: "Y"
default: "N"
information: "Print steps & compatibility at sites"
relations: "EDAM_data:2527 Parameter"
]
boolean: ancseq [
additional: "Y"
default: "N"
information: "Print sequences at all nodes of tree"
relations: "EDAM_data:2527 Parameter"
]
endsection: output