E2

Taiwan Bioinformatics Institute

主辦單位：

Introduction to Molecular Evolution and Phylogenetic Analysis

Phylogenetic Analysis Methods
Nucleotide substitution models
Distance matrix methods

Computer Lab
Phylip home page, BioEdit, Mega, clustalX, Genedoc
Phylogenetic analysis programs (PHYLIP): distance matrix methods

Phylogenetic Analysis Methods
Discrete character methods (Maximum parsimony)
Computer Lab
PHYLIP: Maximum parsimony

Phylogenetic Analysis Methods
Maximum likelihood method

Statistical Test for Phylogenetic Trees
Bootstrap analysis

Computer Lab
PHYLIP: ML, Seqboot

The Other Phylogenetic Analysis Methods
Quartet puzzling method: Likelihood mapping analysis
Bayesian analyses
Split decomposition method

Detecting Recombination in Viral Sequences
Similarity plot, bootscan plot

Computer Lab
Simplot, modeltest, MrBayes, Splits tree

Examples of Applications Using Phylogenetic Analysis

POWER (Phylogenetic Web Repeater)
Power: Graphical interface of PHYLIP programs

Palm (Phylogenetic Reconstruction by Automatic Likelihood Model Selector)
介紹：PALM為一個自動選擇最佳演化模型之生物分子親緣關係分析平台，共有24種DNA演化模型及96種蛋白質演化模型，可供本系統同時評估，依其統計結果擇取最佳模型再輔以Bootstrap分析，並進一步提供互動式親緣樹檢視介面，方便使用者對親緣樹型進行翻轉、交換，同時也可以透過圖像化方式刪除與新增分析序列，再次進行新的分析工作。PLAM以極具親和性的介面，大大地減少使用者的進行複雜多演化模型分析的難度與時間，使得生物學家能以更具統計意義的演化模型來解釋所建構出來的親緣關係，與其中所包含的生物意涵。