Introduction to Phylogenetic Analysis of Molecular Sequence Data

Phylogeny is a model of the relationships between organisms, genes, proteins, or other structures based on common ancestry. It is also used for epidemiological investigations and analysis of parallel evolution between host and parasite. Phylogenetic trees can be visualized as dendrograms or as radial trees. The most important information read from a phylogenetic tree is the location of the different monophyletic groups. The main types of model parameters needed to construct a tree from a given dataset are the tree shape and the substitution matrix. One of the four types of phylogenetic methods (maximum parsimony, neighbor joining, maximum likelihood and Mr. Bayes) can then be used to construct the tree. The strength of trees can be evaluated by bootstrap analysis. The major data formats used as input for phylogenetic programs are presented as well as the major program packages. Finally, the reader is guided to the construct own neighbor joining tree.