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Tree Building Assumptions: Distance-based methods: 1、All sequences involved are homologous. 2、Tree branches are additive. Character-based methods: 1、Characters at corresponding positions in a multiple sequence alignment are homologous among the sequences involved. 2、Each character evolves independently and is treated as an individual evolution unit.
UPGMA Unweighted Pair Group Method with Arithmetic mean Closest pair→ Cluster → Average distances
Page 1 and 2: Molecular Phylogenetics Li Jing Pek
Page 3: Introduction Phylogenetics: The stu
Page 6 and 7: Study of phylogeny A phylogeny is a
Page 8 and 9: Introduction Terminal nodes (leaves
Page 10 and 11: Sister group & Outgroup Sister grou
Page 12 and 13: Polytomy & Dichotomy un-resolved re
Page 14 and 15: Contents 1 Phylogenetics Introducti
Page 16 and 17: Choosing Molecular Markers • Nucl
Page 18 and 19: Choosing Molecular Markers • Geno
Page 20 and 21: Choosing Models of Evolution Nucleo
Page 24 and 25: UPGMA Advantages: 1、Simple and fa
Page 26 and 27: Neighbor Joining (NJ) Advantages: 1
Page 28 and 29: Maximum Parsimony Parsimony is the
Page 30 and 31: Maximum Likelihood • Maximum like
Page 32 and 33: Rooting the Tree A 10 d (A,D) = 10
Page 34 and 35: Tree evaluation • A statistical t
Page 36: Contents 1 Phylogenetics Introducti
Page 39 and 40: Phylip Phylip 有多种不同
Page 41 and 42: Phylip 软件包的应用 1、
Page 43 and 44: 1、双击执行 protdist.exe,
Page 45 and 46: Bootstrap 分析两个用于
Page 48 and 49: Modeltest 3.7 Number of substitutio
Page 50: Acknowledge • Prof. Luo • Prof.

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