A
straightforward phylogenetic analysis consists of four steps:
PHYLOGENETIC DATA ANALYSIS: THE FOUR STEPS
Alignment
•Building the
data model
•Extraction
of a phylogenetic data set
1
Determining
the substitution model
• Substitution rates between bases
• Among-site substitution rate
heterogeneity
• Substitution rates between amino acids
2
Tree
evaluation
•Randomized
Trees (Skewness Test)
•Randomized
Character Data (Permutation Tests)
•Bootstrap
•Likelihood
Ratio Tests
4
Tree
building
Distance-Based
Methods
1.Unweighted
Pair Group Method with Arithmetic
Mean (UPGMA).
Mean (UPGMA).
2.Neighbor
Joining (NJ).
3.Fitch-Margoliash
(FM).
4.Minimum
Evolution (ME).
Character-Based
Methods
1.Maximum
Parsimony (MP).
2.Maximum
Likelihood (ML).
3