Module 8: Phylogenetic Analysis
Distance (Phenetic) Methods
- Distance matrix: Pairwise comparisons of sequence differences are employed to create a matrix of distances
between related sequences. This distance matrix is the basis for constructing the phylogenetic tree. As seen before
(Module 4) the distance between two sequences are calculated as a sum of differences
between them at the molecular level. It is implicit in the algorithm calculating distances that the two sequences
are similar enough to be aligned. The same differences that arise during the construction of DNA and protein
distance matrixes, as discussed in Module 4, are relevant in phylogenetic analysis.
- Clustering algorithms: These methods build a phylogenetic tree by, first, calculating distances between all
sequences from various taxa by pairwise comparisons, and then clustering (grouping) the different pairs successively
going from the least to most distant taxa. UPGMA (Unweighted Pair
Group Method using Arithmetic averages) is a simple and fast algorithm that is being used extensively to build
phylogenetic trees. This method assumes a randomized molecular clock [REF. Sneath, P. H. A. and Sokal, R. R.
(1973) in Numerical Taxonomy, pp. 230-234, W. H. Freeman and Company, San Francisco, CA, USA]
(Figure of a Rooted Tree)
Neighbor-Joining Method is an algorithm that adjusts for
differences in the rate of evolution of each taxon (unlike the UPGMA method which assumes that all taxons evolve at
the same rate). Hence there is no assumption of the molecular clock and the resultant tree is unrooted. [REF.
Saitou and Nei (1987), Mol. Biol.Evol. 4:406] (Figure of an Unrooted Tree)