Bioinformatics and Computational Biology

  1. Phylogenetics and Evolutionary Analysis
    1. Phylogenetic Concepts
      1. Tree Representation
        1. Tree Terminology
          1. Nodes and Branches
            1. Leaves and Internal Nodes
              1. Clades and Monophyly
              2. Tree Types
                1. Rooted Trees
                  1. Unrooted Trees
                    1. Bifurcating vs Multifurcating
                    2. Tree Interpretation
                      1. Evolutionary Relationships
                        1. Time and Distance
                          1. Ancestral States
                        2. Evolutionary Models
                          1. Molecular Evolution
                            1. Neutral Theory
                              1. Selection Pressure
                                1. Molecular Clock Hypothesis
                                2. Substitution Patterns
                                  1. Transitions vs Transversions
                                    1. Synonymous vs Non-synonymous
                                      1. Codon Usage Bias
                                  2. Phylogenetic Reconstruction Methods
                                    1. Distance-Based Methods
                                      1. Distance Matrix Construction
                                        1. Pairwise Distances
                                          1. Evolutionary Distance Models
                                          2. UPGMA Method
                                            1. Clustering Algorithm
                                              1. Molecular Clock Assumption
                                                1. Limitations and Applications
                                                2. Neighbor-Joining Method
                                                  1. Minimum Evolution Principle
                                                    1. Algorithm Steps
                                                      1. Advantages over UPGMA
                                                    2. Character-Based Methods
                                                      1. Maximum Parsimony
                                                        1. Parsimony Principle
                                                          1. Character State Changes
                                                            1. Tree Searching Algorithms
                                                              1. Consensus Methods
                                                              2. Maximum Likelihood
                                                                1. Likelihood Function
                                                                  1. Substitution Models
                                                                    1. Parameter Optimization
                                                                      1. Model Selection
                                                                      2. Bayesian Inference
                                                                        1. Prior Distributions
                                                                          1. Posterior Probability
                                                                            1. Markov Chain Monte Carlo
                                                                              1. Convergence Assessment
                                                                          2. Evolutionary Models
                                                                            1. DNA Substitution Models
                                                                              1. Jukes-Cantor Model
                                                                                1. Equal Substitution Rates
                                                                                  1. Model Assumptions
                                                                                  2. Kimura Two-Parameter Model
                                                                                    1. Transition/Transversion Ratio
                                                                                      1. Rate Heterogeneity
                                                                                      2. General Time Reversible Model
                                                                                        1. Six Substitution Types
                                                                                          1. Rate Matrix
                                                                                          2. Gamma Distribution
                                                                                            1. Rate Variation Among Sites
                                                                                              1. Shape Parameter
                                                                                            2. Protein Evolution Models
                                                                                              1. Empirical Matrices
                                                                                                1. Dayhoff PAM Matrices
                                                                                                  1. JTT Model
                                                                                                    1. WAG Model
                                                                                                    2. Mechanistic Models
                                                                                                      1. Codon-Based Models
                                                                                                        1. Selection Models
                                                                                                    3. Tree Reliability and Validation
                                                                                                      1. Bootstrap Analysis
                                                                                                        1. Resampling Procedure
                                                                                                          1. Bootstrap Support Values
                                                                                                            1. Interpretation Guidelines
                                                                                                            2. Jackknife Analysis
                                                                                                              1. Character Deletion
                                                                                                                1. Support Assessment
                                                                                                                2. Posterior Probabilities
                                                                                                                  1. Bayesian Support
                                                                                                                    1. Credibility Intervals
                                                                                                                    2. Alternative Validation Methods
                                                                                                                      1. Cross-Validation
                                                                                                                        1. Parametric Bootstrap
                                                                                                                      2. Advanced Phylogenetic Analysis
                                                                                                                        1. Molecular Dating
                                                                                                                          1. Relaxed Molecular Clocks
                                                                                                                            1. Calibration Points
                                                                                                                              1. Divergence Time Estimation
                                                                                                                              2. Phylogenetic Networks
                                                                                                                                1. Reticulate Evolution
                                                                                                                                  1. Hybridization Events
                                                                                                                                    1. Horizontal Gene Transfer
                                                                                                                                    2. Ancestral State Reconstruction
                                                                                                                                      1. Character Evolution
                                                                                                                                        1. Ancestral Sequence Inference
                                                                                                                                          1. Evolutionary Scenarios

                                                                                                                                      Previous

                                                                                                                                      7. Proteomics and Structural Bioinformatics

                                                                                                                                      Go to top

                                                                                                                                      Next

                                                                                                                                      9. Systems Biology and Network Analysis