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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.
% 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
Standard (Mandatory) qualifiers: [-sequence] seqset File containing a sequence alignment. [-outseq] seqout [
|Standard (Mandatory) qualifiers||Allowed values||Default|
|File containing a sequence alignment.||Readable set of sequences||Required|
|Sequence filename and optional format (output USA)||Writeable sequence||<*>.format|
|Additional (Optional) qualifiers||Allowed values||Default|
|-name||Name of the consensus sequence||Any string is accepted||An empty string is accepted|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
!!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
>EMBOSS_001 ACGTACGTACGTACGTACGTacgtACGTACGTACGTACGTMSKWMSKWMSKWMSKWMSKW MSKWMSKWMSKWMSKWMSKWACGTACGTACGTACGTACGTACGTACGTWSSWACGTACGT
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:
|cons||Create a consensus sequence from a multiple alignment|
|megamerger||Merge two large overlapping DNA sequences|
|merger||Merge two overlapping sequences|