We are going to draw a phylogenetic tree from the cannabinoid receptor proteins that we have been looking at in the previous tutorials.

First, get the ClustalW alignment of the eleven sequences as demonstrated in the example for ClustalW. Copy the whole ClustalW alignment (including the heading, indicating that it is an alignment in ClustalW format). Then go to the PHYLIP protein method for computing distance matrices. Paste the whole alignment into the text-entry box, and type your e-mail address into the box provided.

This is necessary in case the server is busy, and has to notify you that your analysis is done. Then click on 'Run protdist'.

The next page now has a list of the result files resulting from the protdist analysis. These include the outfile, which contains the matrix of pairwise distances. There is a pull-down menu from which we can use to choose 'neighbor', for example.

This will run a neighbor joining analysis on the output file, yielding a tree file. Then click on 'Run the selected program on outfile'. This brings us directly to the Neighbor page, where we simply click on 'Run Neighbor'.

Now we get another set of output files, of which the treefile is the one that we are looking for.

Click on the treefile link. Copy the plain text contents of this page.

Now go to the Phylodendron home page, and paste the tree file into the main text-entry box. We can choose what style we want the resulting tree to be in, so let's choose 'Phenogram' by clicking on the relevant button.

One note of warning: on some computers, the 'PDF (with hyperlinks)' options causes the Phylodendron server to go into an endless loop. If this happens, your computer IP will be blocked from accessing the site again. To prevent this happening, choose the GIF image output option.

Click on 'Submit'. The tree that we get shows the three type II receptor genes forming a group by themselves embedded in the rest of the type I genes.

Try using other tree making programs from the PHYLIP set of programs, even with the same ClustalW alignment. See if you get the same tree with the different methods of analysis, or not.