infoalign - Display basic information about a multiple sequence alignment

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           Wrote the script used to autogenerate this manual page.

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       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

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EMBOSS 6.4.0                                       05/11/2012                                      INFOALIGN(1e)

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).

       infoalign - Display basic information about a multiple sequence alignment

Inputsection-sequenceseqset
           The sequence alignment to be displayed.

       -matrixmatrix
           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.

       -refseqstring
           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.

   Advancedsection-pluralityfloat
           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

       -identityfloat
           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

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

       -htmlboolean
           Default value: N

       -onlyboolean
           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

       -headingboolean
           Default value: @(!$(only))

       -usaboolean
           Default value: @(!$(only))

       -nameboolean
           Default value: @(!$(only))

       -seqlengthboolean
           Default value: @(!$(only))

       -alignlengthboolean
           Default value: @(!$(only))

       -gapsboolean
           Default value: @(!$(only))

       -gapcountboolean
           Default value: @(!$(only))

       -idcountboolean
           Default value: @(!$(only))

       -simcountboolean
           Default value: @(!$(only))

       -diffcountboolean
           Default value: @(!$(only))

       -changeboolean
           Default value: @(!$(only))

       -weightboolean
           Default value: @(!$(only))

       -descriptionboolean
           Default value: @(!$(only))

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

infoalign-sequenceseqset [-matrixmatrix] [-refseqstring] -pluralityfloat-identityfloat-outfileoutfile [-htmlboolean] -onlyboolean-headingboolean-usaboolean-nameboolean-seqlengthboolean-alignlengthboolean-gapsboolean-gapcountboolean-idcountboolean-simcountboolean-diffcountboolean-changeboolean-weightboolean-descriptionbooleaninfoalign-help