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
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