Python Programming for Biology: Bioinformatics and Beyond

Figure 14.4.  How phylogenetic trees may be used to count substitution events. A

multiple alignment can be used to find sequence differences and thus describe

conservation (or variation) as the proportions of different residues present at a given

position. However, if we consider the evolutionary divergence of the sequences from one

another, as illustrated by a phylogenetic tree, we can get more information about the

evolutionary rate of change. The illustrated trees place the aligned sequences in two

different hypothetical situations. For the first tree only one W

↔Y amino acid substitution

is required to generate the observed sequences, whereas for the second two substitutions

are required. Naturally, the substitutions shown are the simplest scenarios, but overall the

most frugal changes will be the most likely.