Last updated
Last updated
Multiple sequence alignment and phylogenetic analysis allow the identification of conserved positions in protein and nucleic acid sequences. This can lead to an appreciation of the evolutionary history of a group of sequences.
The clustal family of programs is commonly used to produce multiple sequence alignments. Other options are available as well:
There are 3 different ways to use the clustal programs.
Web-based clustalw can be used .
ClustalX GUI (and also the command-line clustalw executable) is available for download .
Command-line clustalw2 is installed on rous
The major difference between the 3 options is the interface and the calculation of bootstrap values for the tree, which is only available in the command-line and GUI versions. Other details of running the program are the same. For this lesson, we will use the web-based version to align these sequences.
Login to rous and copy the clustal training files to your home directory.
enter the clustal directory:
view the raw sequence files:
launch the clustalw application:
Select option 1 to load sequence and specify the file "tiny.pep". Before being returned to the original meny, you should see:
From the original menu, now select option 2. Multiple Alignments. This activates the Alignment menu:
All default options are correct except option 9,select this to see the output format menu:
User toggle #4 to activate PHYLIP output, hit return to revisit the alignment menu
Select option 1 to do the alignment. Accept the default conditions and hit return until you end up at the main menu. Exit the program with "X".
This is the clustal format output:
This is the phylip format output:
The following interactive menu appears, options 1 and 2 will be used in this demonstration. Additional information is available