| consambig

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## Function

Create an ambiguous consensus sequence from a multiple alignment

## Description

cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the amino acid residue or nucleotide at each position is compared to the possible ambiguity codes. The consensus sequence uses the minimum ambiguity code match.

## Algorithm

The ambiguity codes are defined in local data files. consambig uses these files to determine which codes match all residues or nucleotides in the input sequences at each position.

## Usage

Here is a sample session with consambig

    % consambig
    Create an ambiguous consensus sequence from a multiple alignment
    Input (aligned) sequence set: dna.msf
    output sequence [dna.fasta]: aligned.consambig

Go to the input files for this example
Go to the output files for this example

## Command line arguments

    Create an ambiguous consensus sequence from a multiple alignment
    Version: EMBOSS:6.6.0.0

       Standard (Mandatory) qualifiers:
      [-sequence]          seqset     File containing a sequence alignment.
      [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
                                      optional format (output USA)

       Additional (Optional) qualifiers:
       -name               string     Name of the consensus sequence (Any string)

       Advanced (Unprompted) qualifiers: (none)
       Associated qualifiers:

       "-sequence" associated qualifiers
       -sbegin1            integer    Start of each sequence to be used
       -send1              integer    End of each sequence to be used
       -sreverse1          boolean    Reverse (if DNA)
       -sask1              boolean    Ask for begin/end/reverse
       -snucleotide1       boolean    Sequence is nucleotide
       -sprotein1          boolean    Sequence is protein
       -slower1            boolean    Make lower case
       -supper1            boolean    Make upper case
       -scircular1         boolean    Sequence is circular
       -squick1            boolean    Read id and sequence only
       -sformat1           string     Input sequence format
       -iquery1            string     Input query fields or ID list
       -ioffset1           integer    Input start position offset
       -sdbname1           string     Database name
       -sid1               string     Entryname
       -ufo1               string     UFO features
       -fformat1           string     Features format
       -fopenfile1         string     Features file name

       "-outseq" associated qualifiers
       -osformat2          string     Output seq format
       -osextension2       string     File name extension
       -osname2            string     Base file name
       -osdirectory2       string     Output directory
       -osdbname2          string     Database name to add
       -ossingle2          boolean    Separate file for each entry
       -oufo2              string     UFO features
       -offormat2          string     Features format
       -ofname2            string     Features file name
       -ofdirectory2       string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write first file to standard output
       -filter             boolean    Read first file from standard input, write
                                      first file to standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options and exit. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report dying program messages
       -version            boolean    Report version number and exit

Qualifier | Type | Description | Allowed values | Default
--- | --- | --- | --- | ---
Standard (Mandatory) qualifiers
[-sequence] (Parameter 1) | seqset | File containing a sequence alignment. | Readable set of sequences | Required
[-outseq] (Parameter 2) | seqout | Sequence filename and optional format (output USA) | Writeable sequence | <*>.format
Additional (Optional) qualifiers
-name | string | Name of the consensus sequence | Any string |
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-sequence" associated seqset qualifiers
-sbegin1 -sbegin_sequence | integer | Start of each sequence to be used | Any integer value | 0
-send1 -send_sequence | integer | End of each sequence to be used | Any integer value | 0
-sreverse1 -sreverse_sequence | boolean | Reverse (if DNA) | Boolean value Yes/No | N
-sask1 -sask_sequence | boolean | Ask for begin/end/reverse | Boolean value Yes/No | N
-snucleotide1 -snucleotide_sequence | boolean | Sequence is nucleotide | Boolean value Yes/No | N
-sprotein1 -sprotein_sequence | boolean | Sequence is protein | Boolean value Yes/No | N
-slower1 -slower_sequence | boolean | Make lower case | Boolean value Yes/No | N
-supper1 -supper_sequence | boolean | Make upper case | Boolean value Yes/No | N
-scircular1 -scircular_sequence | boolean | Sequence is circular | Boolean value Yes/No | N
-squick1 -squick_sequence | boolean | Read id and sequence only | Boolean value Yes/No | N
-sformat1 -sformat_sequence | string | Input sequence format | Any string |
-iquery1 -iquery_sequence | string | Input query fields or ID list | Any string |
-ioffset1 -ioffset_sequence | integer | Input start position offset | Any integer value | 0
-sdbname1 -sdbname_sequence | string | Database name | Any string |
-sid1 -sid_sequence | string | Entryname | Any string |
-ufo1 -ufo_sequence | string | UFO features | Any string |
-fformat1 -fformat_sequence | string | Features format | Any string |
-fopenfile1 -fopenfile_sequence | string | Features file name | Any string |
"-outseq" associated seqout qualifiers
-osformat2 -osformat_outseq | string | Output seq format | Any string |
-osextension2 -osextension_outseq | string | File name extension | Any string |
-osname2 -osname_outseq | string | Base file name | Any string |
-osdirectory2 -osdirectory_outseq | string | Output directory | Any string |
-osdbname2 -osdbname_outseq | string | Database name to add | Any string |
-ossingle2 -ossingle_outseq | boolean | Separate file for each entry | Boolean value Yes/No | N
-oufo2 -oufo_outseq | string | UFO features | Any string |
-offormat2 -offormat_outseq | string | Features format | Any string |
-ofname2 -ofname_outseq | string | Features file name | Any string |
-ofdirectory2 -ofdirectory_outseq | string | Output directory | Any string |
General qualifiers
-auto | boolean | Turn off prompts | Boolean value Yes/No | N
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N
-warning | boolean | Report warnings | Boolean value Yes/No | Y
-error | boolean | Report errors | Boolean value Yes/No | Y
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y
-die | boolean | Report dying program messages | Boolean value Yes/No | Y
-version | boolean | Report version number and exit | Boolean value Yes/No | N

## Input file format

The USA of a set of aligned sequences.

### Input files for usage example

### File: dna.msf

    !!NA_MULTIPLE_ALIGNMENT

     dna.msf  MSF: 120  Type: N  January 01, 1776  12:00  Check: 3196 ..

     Name: MSFM1          Len:   120  Check:  8587  Weight:  1.00
     Name: MSFM2          Len:   120  Check:  6178  Weight:  1.00
     Name: MSFM3          Len:   120  Check:  8431  Weight:  1.00

    //

            MSFM1  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC
            MSFM2  ACGTACGTAC GTACGTACGT ....ACGTAC GTACGTACGT ACGTACGTAC
            MSFM3  ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT CGTACGTACG

            MSFM1  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
            MSFM2  GTACGTACGT ACGTACGTAC GTACGTACGT ACGTACGTAC GTACGTACGT
            MSFM3  TACGTACGTA CGTACGTACG TACGTACGTA ACGTACGTAC GTACGTACGT

            MSFM1  ACGTACGTAC GTACGTACGT
            MSFM2  ACGTACGTTG CAACGTACGT
            MSFM3  ACGTACGTAC GTACGTACGT

## Output file format

The output consists of a sequence file holding the consensus sequence.

### Output files for usage example

### File: aligned.consambig

    >EMBOSS_001
    ACGTACGTACGTACGTACGTacgtACGTACGTACGTACGTMSKWMSKWMSKWMSKWMSKW
    MSKWMSKWMSKWMSKWMSKWACGTACGTACGTACGTACGTACGTACGTWSSWACGTACGT

## Data files

consambig uses the standard files Ebases.iub and Eresidues.iub in the EMBOSS data directory.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
cons | Create a consensus sequence from a multiple alignment
megamerger | Merge two large overlapping DNA sequences
merger | Merge two overlapping sequences

## Author(s)

Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.

## History

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments

None