Provided by: emboss_6.6.0+dfsg-7ubuntu2_amd64
infoalign - Display basic information about a multiple sequence alignment
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
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).
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 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).
infoalign is fully documented via the tfm(1) system.
Debian Med Packaging Team <firstname.lastname@example.org> Wrote the script used to autogenerate this manual page.
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.