7.6.3. Building trees using distance and character based methods
To assess the reliability of
the tree topology, users should be aware of the phylogenetic tree construction
and tree analysis methods according to the data and algorithmic strategy
used. Each method has different assumptions
that may or may not be valid for the evolutionary process of the given sequence
data. For example, the distance based method UPGMA (Unweighted Pair Group
Method with Arithmetic mean) assumes a neutral mutation rate proportional to
time (a molecular clock). Therefore, it is important to be aware of this fact
when evaluating tree topology generated by each method. It is encouraged that
one run a variety of distance based methods (NeighbourJoining, UPGMA, Minimum
Evolution) that calculate evolutionary distance between sequences, and character
based methods (Maximum Parsimony, Maximum Likelihood, Bayesian) that determine
the most probable evolutionary event history between sequences (Table 1).
Table
1. Classification of phylogenetic analysis
methods and strategies.
Tree building strategy 
Method 


Distance based 
Character based 
Clustering algorithm 
UPGMA 
n/a 
Optimality criterion 
Minimum Evolution 
Maximum Parsimony 
Statistical testing of
topology should also be performed where possible, i.e. bootstrapping
analysis. Altering the substitution
model, rates and patterns, and treatment of gaps/missing data may also be
warranted, though the varying justifications for each of these tests is beyond
the detail provided here. Low branch
support for any topology shown in the final tree or conflicts in topology
determined by multiple testing should be addressed when presenting any phylogenetic
data.