Phylogeny
Introduction
Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.
- Download Software
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 - Input Alignment
Input Window
Phylogeny using an alignment directly entered into the input box in a supported format. Alignment formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW 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 500 sequences and 1MB of data.
File Upload
Phylogeny using an alignment uploaded as a file. Alignment file formats supported include Clustal, FASTA and MSF. Partially formatted or unaligned sequences are not accepted. Adding a return to the end of the sequence may help ClustalW 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 500 sequences and 1MB of data.
Step 2 - Set Your Parameters
Tree format
Determines the outputs that ClustalW produces.
| Format | Description | Value |
|---|---|---|
| Default | Newick/PHYLIP format tree file | phylip |
| Clustal | Clustal format file in addition to the PHYLIP tree | nj |
| Distance Matrix | Distance matrix file in addition to the PHYLIP tree | dist |
| NEXUS | NEXUS format file in addition to the PHYLIP tree | nexus |
Default value is: Default [phylip]
Distance correction
Controls whether ClustalW attempts to correct for multiple substitutions at the same site. This is recommended to be set 'on' for more divergent sequences and has the effect of stretching branch lengths. For very divergent sequences the distances cannot be reliably corrected.
| Type | Value |
|---|---|
| off | false |
| on | true |
Default value is: off [false]
Exclude gaps
With this option enabled columns where any of the sequences in the input have a gap will be excluded, forcing the alignment to use only positions where information can be included from all sequences.
| Type | Value |
|---|---|
| off | false |
| on | true |
Default value is: off [false]
Clustering method
Clustering Methods
| Method | Description | Value |
|---|---|---|
| Neighbour-joining | Uses the neighbour-joining algorithm to construct trees from the distance matrix | Neighbour-joining |
| UPGMA | Uses the faster UPGMA tree construction algorithm | UPGMA |
Default value is: Neighbour-joining
Percent identity matrix
Output the percentage identity matrix
| Type | Value |
|---|---|
| off | false |
| on | true |
Default value is: off [false]
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).