UPGMA (Construct Phylogeny)

Phylogeny | Construct/Test UPGMA Tree…

This command is used to construct a UPGMA tree.  This tree-making method assumes that the rate of evolution has remained constant throughout the evolutionary history of the included taxa A taxon is the individual unit whose evolutionary relationship is being investigated. Depending on the study, “taxa” may refer to species, populations, individuals, or sequences within an individual.RH_Taxa.  Therefore, it produces a rooted tree A rooted tree is one in which the root of the phylogenetic tree is determined by using the mid-point rooting or out-group sequences.RH_Rooted_tree.

If your input data is a distance matrix, then using this command makes MEGA proceed directly to constructing and displaying the UPGMA tree.  In all other instances, you will be asked in an Analysis PreferencesHC_NJ_Analysis_Options dialog box to specify the distance estimation method, subset of sites to include, and whether to conduct a test of the inferred tree A tree reconstructed from the observed sequence or other appropriate data using any tree-making method (such as UPGMA, NJ, ME, or MP) is known as an inferred or reconstructed tree.RH_Inferred_tree.