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B. Building the guide tree.

• There are many ways of building a tree from a matrix of pairwise distances. CLUSTAL W uses the neighbour-joining (NJ) method, which is the most favoured approach these days. Earlier versions of CLUSTAL used the unweighted pair group method using arithmetic averages (UPGMA), and this is still used in some programs.

• A root of the tree is then determined by the so-called mid-point method (giving equal means for the branch lengths on either side of the root).

• The W in CLUSTAL W stands for Weights, an important feature of this program. These are calculated in a straightforward way. They correct for unequal sampling at different evolutionary distances.

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