Clustal Omega

Introduction

Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

FAQs
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How to use this 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 be in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot format. 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. There is currently a limit of 2000 sequences and 2MB of data.

Sequence File Upload

A file containing three or more valid sequences in any format (GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB/Swiss-Prot) can be uploaded and used as input for the multiple sequence alignment. 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. There is currently a limit of 2000 sequences and 2MB of data.

Sequence Type

Defines the type of the sequences to be aligned

Type Value
PROTEIN protein
DNA dna
RNA rna

Step 2 - Set Your Parameters

Dealign Input Sequences

Remove any existing alignment (gaps) from input sequences.

Order Description Abbreviation
no false
yes true

Default value is: no [false]

Output Alignment Format

Format for generated multiple sequence alignment.

Order Description Abbreviation
Clustal w/o numbers Clustal alignment format without base/residue numbering clustal
Clustal w/ numbers Clustal alignment format with base/residue numbering clustal_num
Pearson/FASTA Pearson or FASTA sequence format fa
MSF Multiple Sequence File (MSF) alignment format msf
PHYLIP PHYLIP interleaved alignment format phylip
SELEX SELEX alignment format selex
STOCKHOLM STOCKHOLM alignment format stockholm
VIENNA VIENNA alignment format vienna

Default value is: Clustal w/o numbers [clustal]

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.

Order Description Abbreviation
yes true
no false

Default value is: yes [true]

mBed-like Clustering Iteration

Use mBed-like clustering during subsequent iterations.

Order Description Abbreviation
yes true
no false

Default value is: yes [true]

Number of Combined Iterations

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

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.

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.

Default value is: default [-1]

Order

The order in which the sequences appear in the final alignment

Order Description Abbreviation
aligned Determined by the alignment aligned
input Input order is preserved input

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 joe@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).

References

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
(2011) Molecular systems biology 7 :539
A new bioinformatics analysis tools framework at EMBL-EBI.
(2010 Jul) Nucleic acids research 38 (Web Server issue) :W695-9
Analysis Tool Web Services from the EMBL-EBI.
(2013 Jul) Nucleic acids research 41 (Web Server issue) :W597-600