infoalign1e

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))