Hi,
When I run emboss-6.0.1 'edialign' program on command line, I saw this
error:
Error: File /usr/local/EMBOSS-6.0.1/share/EMBOSS/acd/edialign.acd line
124: (outseq) Attribute 'aligned' unknown
The edialign.acd file was attached.
Thank you.
application: edialign [
documentation: "Local multiple alignment of sequences"
groups: "Alignment:Multiple"
]
section: input [
information: "Input section"
type: "page"
]
seqset: sequences [
parameter: "Y"
type: "any"
aligned: "N"
]
endsection: input
section: additional [
information: "Additional section"
type: "page"
]
list: nucmode [
additional: "$(sequences.nucleic)"
information: "Nucleic acid sequence alignment mode"
help: "Nucleic acid sequence alignment mode (simple, translated or
mixed)"
values: "n: simple; nt: translation; ma: mixed alignments"
default: "n"
]
boolean: revcomp [
additional: "@($(sequences.nucleic) & @($(nucmode) != n))"
information: "Also consider the reverse complement"
default: "N"
]
selection: overlapw [
additional: "Y"
information: "Use overlap weights"
help: "By default overlap weights are used when Nseq =<35 but you
can set this to 'yes' or 'no'"
values: "default (when Nseq =< 35);yes;no"
default: "default (when Nseq =< 35)"
]
list: linkage [
additional: "Y"
information: "Clustering method to construct sequence tree"
help: "Clustering method to construct sequence tree (UPGMA,
minimum linkage or maximum linkage)"
values: "UPGMA: UPGMA; max: maximum linkage; min: minimum
linkage"
default: "UPGMA"
]
integer: maxfragl [
additional: "Y"
information: "Maximum fragment length"
minimum: "0"
default: "40"
]
boolean: fragmat [
additional: "@($(sequences.nucleic) & @($(nucmode) != nt))"
information: "Consider only N-fragment pairs that start
with two matches"
default: "N"
]
integer: fragsim [
additional: "@($(sequences.protein) | @($(nucmode) != n))"
information: "Consider only P-fragment pairs if first amino
acid or codon pair has similarity score of at least n"
minimum: "0"
default: "4"
]
boolean: itscore [
additional: "Y"
information: "Use iterative score"
default: "N"
]
float: threshold [
additional: "Y"
information: "Threshold for considering diagonal for
alignment"
minimum: "0.0"
default: "0.0"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
boolean: mask [
information: "Replace unaligned characters by stars '*'
rather then putting them in lowercase"
default: "N"
]
boolean: dostars [
information: "Activate writing of stars instead of numbers"
default: "N"
]
integer: starnum [
information: "Put up to n stars '*' instead of digits 0-9
to indicate level of conservation"
minimum: "0"
default: "4"
]
outfile: outfile [
parameter: "Y"
knowntype: "edialign output"
]
seqoutall: outseq [
parameter: "Y"
type: "gapany"
aligned: "Y"
]
endsection: output
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