EMBASSY: CLUSTALOMEGA: eomega

eomega

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Function

Multiple sequence alignment (ClustalO wrapper)

Description

eomega is a wrapper to clustalo. It takes a set of unaligned sequences and produces an output alignment.

Clustal-Omega (clustalo) is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of handling data-sets of hundreds of thousands of sequences in reasonable time.

In its current form Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become available in a future version.

Algorithm

Clustal-Omega uses HMMs for the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are optionally made using mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple alignment then proceeds by aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

Usage

Here is a sample session with eomega

% eomega globins.fasta Multiple sequence alignment (ClustalO wrapper) (aligned) output sequence set [globins.aln]:

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

Command line arguments

Multiple sequence alignment (ClustalO wrapper)
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     File containing sequences to align
  [-outseq]            seqoutset  [.] Sequence set filename
                                  and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -indistfile         infile     Pairwise distance matrix input file (skips
                                  distance computation)
   -inguidefile        infile     Guide tree input file (skips distance
                                  computation and guide tree clustering step)
   -dealign            toggle     [N] Dealign input sequences
   -cluster            menu       [mbed] Method (Values: mbed (mBED method);
                                  full (Full slow method); iter (Iteration
                                  used full slower method))
   -maxiterations      integer    [0] Number of (combined guide tree/HMM)
                                  iterations (Integer from 0 to 2000000000)
   -maxgiterations     integer    [2000000000] Maximum guide tree iterations
                                  (Integer from 0 to 2000000000)
   -maxhiterations     integer    [2000000000] Maximum number of HMM
                                  iterations (Integer from 0 to 2000000000)
   -maxseqs            integer    [2000000000] Maximum number of sequences
                                  (Integer from 2 to 2000000000)
   -maxlenseq          integer    [2000000000] Maximum length of sequence
                                  (Integer from 1 to 2000000000)
   -self               toggle     [N] Set options automatically (might
                                  overwrite some options
   -outformat          menu       [fasta] Format (Values: fasta (FASTA);
                                  clustal (Aln clustal); msf (MSF); phylip
                                  (Phylip); selex (Selex); stockholm
                                  (Stockholm); vienna (ViennaRNA))
   -outdistfile        outfile    [*.eomega] Pairwise distance matrix output
                                  file, only available in cluster mode 'full'
   -outguidefile       outfile    [*.eomega] Guide tree output file
   -log                toggle     [N] Log progress to standard output if not
                                  used for output

   Associated qualifiers:

   "-sequences" 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

   "-outdistfile" associated qualifiers
   -odirectory         string     Output directory

   "-outguidefile" associated qualifiers
   -odirectory         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

[-sequences]
(Parameter 1) seqset File containing sequences to align Readable set of sequences Required

[-outseq]
(Parameter 2) seqoutset Sequence set filename and optional format (output USA) Writeable sequences <*>.format

Additional (Optional) qualifiers

(none)

Advanced (Unprompted) qualifiers

-indistfile infile Pairwise distance matrix input file (skips distance computation) Input file Required

-inguidefile infile Guide tree input file (skips distance computation and guide tree clustering step) Input file Required

-dealign toggle Dealign input sequences Toggle value Yes/No No

-cluster list Method
mbed (mBED method)
full (Full slow method)
iter (Iteration used full slower method)
mbed

-maxiterations integer Number of (combined guide tree/HMM) iterations Integer from 0 to 2000000000 0

-maxgiterations integer Maximum guide tree iterations Integer from 0 to 2000000000 2000000000

-maxhiterations integer Maximum number of HMM iterations Integer from 0 to 2000000000 2000000000

-maxseqs integer Maximum number of sequences Integer from 2 to 2000000000 2000000000

-maxlenseq integer Maximum length of sequence Integer from 1 to 2000000000 2000000000

-self toggle Set options automatically (might overwrite some options Toggle value Yes/No No

-outformat list Format
fasta (FASTA)
clustal (Aln clustal)
msf (MSF)
phylip (Phylip)
selex (Selex)
stockholm (Stockholm)
vienna (ViennaRNA)
fasta

-outdistfile outfile Pairwise distance matrix output file, only available in cluster mode 'full' Output file <*>.eomega

-outguidefile outfile Guide tree output file Output file <*>.eomega

-log toggle Log progress to standard output if not used for output Toggle value Yes/No No

Associated qualifiers

"-sequences" associated seqset qualifiers

-sbegin1
-sbegin_sequences integer Start of each sequence to be used Any integer value 0

-send1
-send_sequences integer End of each sequence to be used Any integer value 0

-sreverse1
-sreverse_sequences boolean Reverse (if DNA) Boolean value Yes/No N

-sask1
-sask_sequences boolean Ask for begin/end/reverse Boolean value Yes/No N

-snucleotide1
-snucleotide_sequences boolean Sequence is nucleotide Boolean value Yes/No N

-sprotein1
-sprotein_sequences boolean Sequence is protein Boolean value Yes/No N

-slower1
-slower_sequences boolean Make lower case Boolean value Yes/No N

-supper1
-supper_sequences boolean Make upper case Boolean value Yes/No N

-scircular1
-scircular_sequences boolean Sequence is circular Boolean value Yes/No N

-squick1
-squick_sequences boolean Read id and sequence only Boolean value Yes/No N

-sformat1
-sformat_sequences string Input sequence format Any string

-iquery1
-iquery_sequences string Input query fields or ID list Any string

-ioffset1
-ioffset_sequences integer Input start position offset Any integer value 0

-sdbname1
-sdbname_sequences string Database name Any string

-sid1
-sid_sequences string Entryname Any string

-ufo1
-ufo_sequences string UFO features Any string

-fformat1
-fformat_sequences string Features format Any string

-fopenfile1
-fopenfile_sequences string Features file name Any string

"-outseq" associated seqoutset 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

"-outdistfile" associated outfile qualifiers

-odirectory string Output directory Any string

"-outguidefile" associated outfile qualifiers

-odirectory 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

eomega reads a set of unaligned sequences and optional distance and guide tree files.

Input files for usage example

File: globins.fasta

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

Output file format

eomega writes alignments using the default Clustal-Omega output.

Output files for usage example

File: globins.aln

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
--------VHLTPEEKSAVTALWGKVNV--DEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLK--G---TFATLSELHCDKLHVDPENFRL
LGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
--------VQLSGEEKAAVLALWDKVNE--EEVGGEALGRLLVVYPWTQRFFDSFGDLSN
PGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLK--G---TFAALSELHCDKLHVDPENFRL
LGNVLVVVLARHFGKDFTPELQASYQKVVAGVANALAHKYH------
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
---------VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDL---
---SHGSAQVKGHGKKVADALTNAVAHVDDMP--N---ALSALSDLHAHKLRVDPVNFKL
LSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
---------VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDL---
---SHGSAQVKAHGKKVGDALTLAVGHLDDLP--G---ALSNLSDLHAHKLRVDPVNFKL
LSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSKYR------
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
---------VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
EAEMKASEDLKKHGVTVLTALGAILKKKGHHE--A---ELKPLAQSHATKHKIPIKYLEF
ISEAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTE--KMSMKLRDLSGKHAKSFQVDPQYFKV
LAAVIADTVAA---------GDAGFEKLMSMICILLRSAY-------
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
--------GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSE
--VPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGV-ADAHFPV
VKEAILKTIKEVVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA---

Data files

None.

Notes

In the clustal-omega README file, this is input option (a).

References

[1] Johannes Soding (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (7): 951–960.

[2] Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol. 2010 May 14;5:21.

[3] http://www.genetics.wustl.edu/eddy/software/#squid

[4] Wilbur and Lipman, 1983; PMID 6572363

[5] Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.

[6] Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.

[7] Kimura M (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences". Journal of Molecular Evolution 16: 111–120.

[8] Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Program name	Description
edialign	Local multiple alignment of sequences
emma	Multiple sequence alignment (ClustalW wrapper)
eomegapp	Profile with profile (ClustalO wrapper)
eomegaps	Single sequence with profile (ClustalO wrapper)
eomegash	Sequence with HMM (ClustalO wrapper)
eomegasp	Sequence with profile (ClustalO wrapper)
infoalign	Display basic information about a multiple sequence alignment
mse	Multiple sequence editor
plotcon	Plot conservation of a sequence alignment
prettyplot	Draw a sequence alignment with pretty formatting
showalign	Display a multiple sequence alignment in pretty format
tranalign	Generate an alignment of nucleic coding regions from aligned proteins

Author(s)

Alan Bleasby
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

None

Wiki

Function

Description

Algorithm

Usage

Command line arguments

Input file format

Input files for usage example

File: globins.fasta

Output file format

Output files for usage example

File: globins.aln

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

History

Target users

Comments