infoaligne - Online in the Cloud

PROGRAM:

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))

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