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
- Official Website
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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 10000 sequences and 5MB 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 |
| NEXUS | NEXUS alignment format | nexus |
| 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).