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INFOALIGN(1e) EMBOSS Manual for Debian 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.
 
05/11/2012 EMBOSS 6.4.0