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Introduction

Clustal Omega is a multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms. 

Official Website

        Clustal Omega website

Download software

        HTTP Download

Important Note

  • We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with EMBL-EBI's Terms of Use. Please contact us if you need further information.

How to Access Clustal Omega

Clustal Omega can be accessed via

Web Form

Web interface for Clustal Omega is available at : https://www.ebi.ac.uk/Tools/msa/clustalo/

How to use the tool

Running a tool from the web form is a simple multiple steps process, starting at the top of the page and following the steps to the bottom.

Each tool has at least 2 steps, but most of them have more:

  • The first steps are usually where the user sets the tool input (e.g. sequences, databases...)
  • In the following steps, the user has the possibility to change the default tool parameters
  • And finally, the last step is always the tool submission step, where the user can specify a title to be associated with the results and an email address for email notification. Using the submit button will effectively submit the information specified previously in the form to launch the tool on the server

Note that the parameters are validated prior to launching the tool on the server and in the event of a missing or wrong combination of parameters, the user will be notified directly in the form.

Step 1 - Sequence

Sequence Input Window

Three or more sequences to be aligned can be entered directly into this box. Sequences can be in GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR/NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only) format.  (See example input formats). Partially formatted sequences are not accepted. Adding a return to the end of the sequence may help certain applications understand the input. Note that directly using data from word processors may yield unpredictable results as hidden/control characters may be present.

Sequence File Upload

A file containing three or more valid sequences in any format (GCG, FASTA, EMBL (Nucleotide only), GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot (Protein only)) can be uploaded and used as input for the multiple sequence alignment. (See example input formats). Word processor files may yield unpredictable results as hidden/control characters may be present in the files. It is best to save files with the Unix format option to avoid hidden Windows characters. 

Sequence Type

Defines the type of the sequences to be aligned

TypeValue
PROTEINprotein
DNAdna
RNArna

Step 2 - Set Your Parameters

Dealign Input Sequences

Remove any existing alignment (gaps) from input sequences.

OrderDescriptionAbbreviation
noEnable de-alignment of input sequencesfalse
yes
true

Default value is: no [false]

Output Alignment Format

Format for generated multiple sequence alignment. (See example output formats).

OrderDescriptionAbbreviation
ClustalW with character counts

Clustal alignment format with base/residue numbering

clustal_num
ClustalWClustal alignment format without base/residue numberingclustal
Pearson/FASTAPearson or FASTA sequence formatfa
MSFMultiple Sequence File (MSF) alignment formatmsf
NEXUSNEXUS alignment formatnexus
PHYLIPPHYLIP interleaved alignment formatphylip
SELEXSELEX alignment formatselex
STOCKHOLMSTOCKHOLM alignment formatstockholm
VIENNAVIENNA alignment formatvienna

Default value is: ClustalW with character counts [clustal_num]

mBed-like Clustering Guide-tree

This option uses a sample of the input sequences and then represents all sequences as vectors to these sequences, enabling much more rapid generation of the guide tree, especially when the number of sequences is large.

OrderDescriptionAbbreviation
yesEnable mbed-like clustering guide-treetrue
no
false

Default value is: yes [true]

mBed-like Clustering Iteration

Use mBed-like clustering during subsequent iterations.

OrderDescriptionAbbreviation
yesEnable mbed-like clustering iterationtrue
no
false

Default value is: yes [true]

Number of Combined Iterations

Number of (combined guide-tree/HMM) iterations. Values 0-5.

Default value is: default(0) [0]

Max Guide Tree Iterations

Having set the number of combined iterations, this parameter can be changed to limit the number of guide tree iterations within the combined iterations. Values - 1 (off) or 1-5.

Default value is: default [-1]

Max HMM Iterations

Having set the number of combined iterations, this parameter can be changed to limit the number of HMM iterations within the combined iterations. Values - 1 (off) or 1-5.

Default value is: default [-1]

Order

The order in which the sequences appear in the final alignment

OrderDescriptionAbbreviation
alignedDetermined by the alignmentaligned
inputInput order is preservedinput

Default value is: aligned

Step 3 - Submission

Job title

It's possible to identify the tool result by giving it a name. This name will be associated to the results and might appear in some of the graphical representations of the results.

Email Notification

Running a tool is usually an interactive process, the results are delivered directly to the browser when they become available. Depending on the tool and its input parameters, this may take quite a long time. It's possible to be notified by email when the job is finished by simply ticking the box "Be notified by email". An email with a link to the results will be sent to the email address specified in the corresponding text box. Email notifications require valid email addresses.

Email Address

If email notification is requested, then a valid Internet email address in the form email@example.org must be provided. This is not required when running the tool interactively (The results will be delivered to the browser window when they are ready).

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Web Services

Web Services are available using REST and SOAP protocols that enable programmatic access and allow their integration into other applications and analytical workflows and pipelines. 

For an introduction on how to run these clients and use them in workflows please see the webinar series.


REST API

The Representational State Transfer (REST) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

LanguageDownloadRequirements

Perl

clustalo.pl

LWP and XML::Simple

Python

clustalo.py

xmltramp2

Third party clients

Third-party clients can be downloaded from the list below. For details of how to use the third-party clients, please contact the client authors directly. We do not provide technical support for the third-party clients.

LanguageDownloadRequirementsAuthor & Contact

Python 2.7

clustalo_urllib_python27.py

urllib2 and xmltrampManavalan Gajapathy (g.manavalan[at]yahoo.co.in)

For details see Environment setup for REST Web Services and Examples for Perl REST Web Services Clients pages.

WADL

The WADL for the Clustal Omega (REST) service: http://www.ebi.ac.uk/Tools/services/rest/clustalo?wadl


 List Tool Parameters

Parameters

Command line parameter

Description

DEALIGN INPUT SEQUENCES--dealignEnable de-alignment of input sequences
MAX GUIDE TREE ITERATIONS--gtiterationsMaximum guide tree iterations
MAX HMM ITERATIONS--hmmiterationsMaximum HMM iterations
MBED-LIKE CLUSTERING GUIDE TREE--mbed Enable mbed-like clustering guide-tree.
MBED-LIKE CLUSTERING ITERATIONS--mbediterationEnable mbed-like clustering iteration
NUMBER OF COMBINED ITERATIONS--iterationsNumber of (combined guide-tree/HMM) iterations
ORDER--orderThe order in which the sequences appear in the final alignment 

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SOAP API

The Simple Object Access Protocol (SOAP) sample clients are provided for a number of programming languages. For details of how to use these clients, download the client and run the program without any arguments.

WSDL

The WSDL for the Clustal Omega (SOAP) service: http://www.ebi.ac.uk/Tools/services/soap/clustalo?wsdl


 List Methods
MethodsDescriptionArgumentsReturns

getParameters()

Get a list of the parameter namesnonea list of strings giving the names of the parameters.

getParameterDetails(parameterId)

Get details of a specific parameterparameterId: identifier/name of the parameter to fetch details ofa wsParameterDetails describing the parameter and its values.

run(email, title, params)

Submit a job to the service

email: (required) user e-mail address. See Why do you need my e-mail address?

title: job title. Default: ””

params: (required) parameters for the tool. These are described by the InputParameters data structure.

a string containing the job identifier (jobId).

getStatus(jobId)

Get the status of a submitted job.jobId: (required) job identifier.

a string containing the status.

The values for the status are:


RUNNING: the job is currently being processed.

FINISHED: job has finished, and the results can then be retrieved.

ERROR: an error occurred attempting to get the job status.

FAILURE: the job failed.

NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: Job Dispatcher.

getResultTypes(jobId)

Get the available result types for a finished jobjobId: (required) job identifier.a list of wsResultType data structures describing the available result types.

getResult(jobId, type, parameters)

Get the result of a job of the specified type.

jobId: (required) job identifier.

type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.

parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.



 List Datatypes

InputParameters

The input parameters for the job:

Attribute

Type

Description

stypestringinput sequence type
guidetreeoutbooleanenable/disable output of guide tree (guide tree generation requires that the “mBed-like clustering guide-tree” is disabled)
dismatoutbooleanenable/disable output of distance matrix (distance matrix generation requires that the “mBed-like clustering guide-tree” is disabled)
dealignbooleanenable/disable gap removal for input sequences (de-alignment)
mbedbooleanenable/disable mBed-like clustering guide-tree
mbediterationbooleanenable/disable mBed-like clustering iteration
iterationsintnumber of iterations
gtiterationsintmaximum guild tree iterations
hmmiterationsintmaximum HMM iterations
outfmtstringoutput alignment format
sequencestringsequences to align

More detailed information about each parameter, including valid values can be obtained using the getParameterDetails(parameterId) operation.

wsParameterDetails

Descriptive information about a tool parameter. Returned by getParameterDetails(parameterId).

Attribute

Type

Description

namestringName of the parameter.
descriptionstringDescription of the parameter, suitable for use in option help interfaces.
typestringData type of the parameter.
valueslist of wsParameterValueList of valid values for the option.

wsParameterValue

Description of a tool parameter value. Used in wsParameterDetails.

Attribute

Type

Description

labelstringDisplay name of the value, for use in interfaces.
valuestringString representation of the value to be passed to the tool parameter.
defaultValuebooleanFlag indicating if this value is the default.
propertieslist of wsPropertyList of key/value pairs providing further information.

wsProperty

Properties of a tool parameter value. Used in wsParameterValue.

Attribute

Type

keystring
valuestring

wsRawOutputParameter

Additional parameters passed when requesting a result. See getResult(jobId, type, parameters).

Attribute

Type

namestring
valuelist of string

wsResultType

Description of a result type. Returned by getResultTypes(jobId).

Attribute

Type

Description

identifierstringIdentifier for the result type. Passed as type to getResult(jobId, type, parameters).
labelstringDisplay name for use in user interfaces.
descriptionstringDescription of the result type, for use in help interfaces.
mediaTypestringMIME type of the returned data.
fileSuffixstringSuggested suffix for file name, if writing data to disk.

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Open API Interface

https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=clustalo


 List Endpoints

Endpoints

DescriptionArgumentsReturns
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameters
Get a list of the parameter names.noneA list of strings giving the names of the parameters.

https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/guidetreeout
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/dismatout
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/dealign
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/mbed
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/mbediteration
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/iterations
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/gtiterations

https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/hmmiterations

https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/outfmt

https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/order
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/stype
https://www.ebi.ac.uk/Tools/services/rest/clustalo/parameterdetails/sequence
Get details of a specific parameter.parameterdetail: identifier/name of the parameter to fetch details of.A wsParameterDetails describing the parameter and its values.
https://www.ebi.ac.uk/Tools/services/rest/clustalo/run 
Submit a job to the service.

email: (required) user e-mail address. See Why do you need my e-mail address?

title: job title. Default: ””.

params: (required) parameters for the tool. These are described by the InputParameters data structure.

A string containing the job identifier (jobId).
https://www.ebi.ac.uk/Tools/services/rest/clustalo/status/<jobid>
Get the status of a submitted job.jobId: (required) job identifier.

A string containing the status.

The values for the status are:

  • RUNNING: the job is currently being processed.

  • FINISHED: job has finished, and the results can then be retrieved.

  • ERROR: an error occurred attempting to get the job status.

  • FAILURE: the job failed.

  • NOT_FOUND: the job cannot be found.

Further details can be found in Synchronous and Asynchronous Access: Job Dispatcher.

https://www.ebi.ac.uk/Tools/services/rest/clustalo/resulttypes/<jobid>
Get the available result types for a finished job.

jobId: (required) job identifier.

Returns: a list of wsResultType data structures describing the available result types.
https://www.ebi.ac.uk/Tools/services/rest/clustalo/result/<jobid>/out
https://www.ebi.ac.uk/Tools/services/rest/clustalo/result/<jobid>/sequence
https://www.ebi.ac.uk/Tools/services/rest/clustalo/result/<jobid>/aln-clustal_num
https://www.ebi.ac.uk/Tools/services/rest/clustalo/result/<jobid>/phylotree
https://www.ebi.ac.uk/Tools/services/rest/clustalo/result/<jobid>/pim
Get the result of a job of the specified type.

jobId: (required) job identifier.

type: (required) string specifying the result type to fetch. See getResultTypes(jobId) for details of the available types.

parameters: optional list of wsRawOutputParameter used to provide additional parameters for derived result types.

Returns: the result data for the specified type, base64 encoded. Depending on the SOAP library and programming language used the result may be returned in decoded form. For some result types (e.g. images) this will be binary data rather than a text string.

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Common Workflow Language

CWL (Common Workflow Language) implementation for consuming EMBL-EBI Bioinformatics Web Services tools' clients are available at https://github.com/ebi-wp/webservice-cwl

For details, see CWL Workflows page. 

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Reference 

Clustal Omega

EBI  Web Services

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