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.