Phylogeny

Introduction

Commonly used phylogenetic tree generation methods provided by the ClustalW2 program.

FAQs
Official Website
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).

References

Clustal W and Clustal X version 2.0.
(2007 Nov 01) Bioinformatics (Oxford, England) 23 (21) :2947-8
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
(1987 Jul) Molecular biology and evolution 4 (4) :406-25
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
(1980 Dec) Journal of molecular evolution 16 (2) :111-20
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