---
name: "infoalign"
section: "1e"
platform: "linux"
package: "emboss"
version: "6.6.0+dfsg-15"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/infoalign"
---

# infoalign(1e)

Display basic information about a multiple sequence alignment

## 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.