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infoalign(1e)


NAME

   infoalign - Display basic information about a multiple sequence
   alignment

SYNOPSIS

   infoalign -sequence seqset [-matrix matrix] [-refseq string]
             -plurality float -identity float -outfile outfile
             [-html boolean] -only boolean -heading boolean -usa boolean
             -name boolean -seqlength boolean -alignlength boolean
             -gaps boolean -gapcount boolean -idcount boolean
             -simcount boolean -diffcount boolean -change boolean
             -weight boolean -description boolean

   infoalign -help

DESCRIPTION

   infoalign is a command line program from EMBOSS ("the European
   Molecular Biology Open Software Suite"). It is part of the
   "Alignment:Multiple,Data retrieval:Sequence data" command group(s).

OPTIONS

   Input section
   -sequence seqset
       The sequence alignment to be displayed.

   -matrix matrix
       This is the scoring matrix file used when comparing sequences. By
       default it is the file 'EBLOSUM62' (for proteins) or the file
       'EDNAFULL' (for nucleic sequences). These files are found in the
       'data' directory of the EMBOSS installation.

   -refseq string
       If you give the number in the alignment or the name of a sequence,
       it will be taken to be the reference sequence. The reference
       sequence is the one against which all the other sequences are
       compared. If this is set to 0 then the consensus sequence will be
       used as the reference sequence. By default the consensus sequence
       is used as the reference sequence.

   Advanced section
   -plurality float
       Set a cut-off for the % of positive scoring matches below which
       there is no consensus. The default plurality is taken as 50% of the
       total weight of all the sequences in the alignment. Default value:
       50.0

   -identity float
       Provides the facility of setting the required number of identities
       at a position for it to give a consensus. Therefore, if this is set
       to 100% only columns of identities contribute to the consensus.
       Default value: 0.0

   Output section
   -outfile outfile
       If you enter the name of a file here then this program will write
       the sequence details into that file.

   -html boolean
       Default value: N

   -only boolean
       This is a way of shortening the command line if you only want a few
       things to be displayed. Instead of specifying: '-nohead -nousa
       -noname -noalign -nogaps -nogapcount -nosimcount -noidcount
       -nodiffcount -noweight' to get only the sequence length output, you
       can specify '-only -seqlength' Default value: N

   -heading boolean
       Default value: @(!$(only))

   -usa boolean
       Default value: @(!$(only))

   -name boolean
       Default value: @(!$(only))

   -seqlength boolean
       Default value: @(!$(only))

   -alignlength boolean
       Default value: @(!$(only))

   -gaps boolean
       Default value: @(!$(only))

   -gapcount boolean
       Default value: @(!$(only))

   -idcount boolean
       Default value: @(!$(only))

   -simcount boolean
       Default value: @(!$(only))

   -diffcount boolean
       Default value: @(!$(only))

   -change boolean
       Default value: @(!$(only))

   -weight boolean
       Default value: @(!$(only))

   -description boolean
       Default value: @(!$(only))

BUGS

   Bugs can be reported to the Debian Bug Tracking system
   (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
   (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

   infoalign is fully documented via the tfm(1) system.

AUTHOR

   Debian Med Packaging Team
   <debian-med-packaging@lists.alioth.debian.org>
       Wrote the script used to autogenerate this manual page.

COPYRIGHT

   This manual page was autogenerated from an Ajax Control Definition of
   the EMBOSS package. It can be redistributed under the same terms as
   EMBOSS itself.



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