Note that we have unaligned protein sequences in FASTA-format in this computer exercise, so they should be aligned before you can make a phylogenetic tree! To do this, first paste the sequences in the EBI ClustalW page and align them. To make a phylogenetic tree, paste the aligned sequences in the submission form on the EBI Phylogeny page, including the first line (the line that says CLUSTAL 2.1 multiple sequence alignment). The aligned sequences can also be downloaded by clicking on the file links (top of clustalW result page). It would of course be better if the EBI server would align the sequences automatically before making a tree, but unfortunately it doesn't do this. The phylogeny software can generate a tree with unaligned sequences, so you should remember yourself to do the alignment first. Remember the guide tree in the alignment page is not a
phylogenetic tree, but one made based on pairwise distances and UPGMA method. The guide tree is a "guide" to
generate the multiple alignment.
The phylogenetic tree you get from EBI server (scroll down the page to see it) is a phylogram, to get a cladogram press the button Show as Cladogram Tree.
From these two figures, can you tell the difference between a cladogram and a phylogram? Both are phylogenetic trees, but a phylogram does not only indicate the relationships between the taxa, it also conveys a sense of time or rate of evolution. The temporal aspect of a phylogram is missing from a cladogram.Remember these trees that you obtain are UNROOTED trees. To make a rooted tree one has to use an outgroup, for example yeast ubiquitin in this example.