Creating a Phylogenetic Tree for Twelve Species :: Phylogenetic Analysis (Bioinformatics Toolbox)

Bioinformatics Toolbox

Creating a Phylogenetic Tree for Twelve Species

Plotting a simple phylogenetic tree for five species seems to indicate a number of monophyletic groups(see Creating a Phylogenetic Tree for Five Species). After a preliminary analysis with five species, you can add more species to your phylogenetic tree. Adding more species to the data set will help you to confirm the groups are valid.

Add more sequences to a MATLAB structure. For example, add mtDNA D-loop sequences for other hominid species.

data2 = {'Puti_Orangutan'          'AF451972';
         'Jari_Orangutan'          'AF451964';
         'Western_Lowland_Gorilla' 'AY079510';
         'Eastern_Lowland_Gorilla' 'AF050738';
         'Chimp_Schweinfurthii'    'AF176722';
         'Chimp_Vellerosus'        'AF315498';
         'Chimp_Verus'             'AF176731';
       };

Get additional sequence data from the GenBank database, and copy the data into the next indices of a MATALB structure.

for ind = 1:7
    seqs(ind+5).Header   = data2{ind,1};
    seqs(ind+5).Sequence = getgenbank(data2{ind,2},
                                      'sequenceonly', true);
end

Calculate pairwise distances and the hierarchical linkage.

distances = seqpdist(seqs,'Method','Jukes-Cantor','Alpha','DNA');
tree = seqlinkage(distances,'UPGMA',seqs);

Draw a phylogenetic tree.
```
h = plot(tree,'orient','bottom');
ylabel('Evolutionary distance')
set(h.terminalNodeLabels,'Rotation',-45)
```
MATLAB draws a phylogenetic tree in a figure window. You can see four main clades for humans, gorillas, chimpanzee, and orangutans.

Creating a Phylogenetic Tree for Five Species

Exploring the Phylogenetic Tree