Download Practical theory (15-20 min) A phylogeny is the representation of the

Practical theory (15-20 min)
A phylogeny is the representation of the evolutionary relationships among groups of sequences, usually from
different organisms. Phylogenies can be given as an output after aligning a group of sequences in some web
applicatios
(.ph
format),
such
as
in
Trex-Online
(http://www.trex.uqam.ca/),
T-Coffee
(http://www.ebi.ac.uk/Tools/msa/tcoffee/), and UniProt (http://www.uniprot.org/). They can also be build using
different web tools, such as TreeDraw. In Phylodendron web page (http://iubio.bio.indiana.edu/treeapp/treeprintform.html) and in ETE toolkit (http://etetoolkit.org/treeview/) different types of trees can be built starting from its
.dnd file.
To build a tree in Trex-Online using the following sequences, first they have to be aligned. Go to “Sequence
alignment > ClustalW”, paste them and submit the job (“Align sequences”).
3-1.fasta
The built tree can be downloaded in Newick format or visualized using the Trex online app. The visualization options
allow the user to build the tree in a hierarchical, axial or radial way, as well as to root it using one sequence as the
root. This option is usually used when a sequence is too distant from the others or to see the relationships between
all of the sequences and a query of interest.
Hierarchical horizontal (root: Clostridium_sp.)
Radial (root: Clostridium_sp.)
The “Proportional edge lengths” options allows to change the tree from a cladogram to a phylogram. A reminder:

Cladogram: tree that shows the relations among sequences. The branches are all the same length.

Phylogram: tree that shows the relations and distances among sequences. The length of the branches are
proportional to the distance between two sequences.
To build their phylogenetic tree in T-Coffee, paste them and submit the job. Once the job is finished, clicking in
“Phylogenetic Tree” allows the user to visualize and download the built tree. It could be visualized as a cladogram
(“Cladogram”) or as a Phylogram (“Real”), depending on the user's needs. When a branch has length = 0, those
sequences are exactly the same. The bigger the distance is, the more separate in evolution the sequences are.
One important feature to take into account when revising a tree is the coherence with the evolution. If we are
building a tree from one protein family (search for orthologs), a mouse sequence should be nearer to a human
sequence than to a worm one. If not, either the sequences are wrong annotated or an evolutionary process
happened, like a horizontal gene transfer (HGT).
Tree of life (numbers are organisms) Tree of protein X (numbers are proteins)
Practical exercises (25-30 min)
6. Using “seq4.fasta” and “seq5.fasta”, find their orthologs in UniProt in Mus musculus, Gallus gallus, Xenopus
laevis and Ornithorhynchus anatinus (platypus). Put all of the sequences in one file and built a phylogenetic tree
using Trex. Use the radial representation of the tree. What do you observe?
7. All of the sequences in “seq6.fasta” are homologs. How many groups of orthologs are there? Which sequence
belong to each group? Is any sequence wrongly annotated?