Bioinformatics

1. Evolutionary Bioinformatics
   1. Comparative Genomics
      1. Methods for species comparison
         1. Alignment-free methods
         2. Genome synteny analysis
         3. Orthologous gene identification
      2. Evolutionary rate estimation
         1. dN/dS ratio analysis
         2. Codon substitution models
      3. Genome rearrangements
         1. Inversions
         2. Translocations
         3. Duplications and deletions
   2. Molecular Evolution Studies
      1. Sequence evolution models
         1. Jukes-Cantor model
         2. Kimura two-parameter model
         3. GTR model
      2. Mutation rate estimation
         1. Molecular clocks
         2. Calibration techniques
      3. Adaptive evolution
         1. Positive selection detection
         2. Balancing selection
      4. Neutral theory of molecular evolution
         1. Concepts and implications
         2. Neutral vs. nearly neutral theory
   3. Phylogenetic Analysis
      1. Tree reconstruction methods
         1. Distance-based methods
         2. Character-based methods
         3. Bayesian inference
      2. Tree visualization techniques
         1. Circular and radial layouts
         2. Cladograms vs. phylograms
      3. Molecular dating
         1. Fossil record integration
         2. Relaxed clock models
      4. Ancestral state reconstruction
         1. Maximum likelihood estimation
         2. Bayesian approaches
   4. Population Genetics
      1. Genetic diversity metrics
         1. Heterozygosity
         2. Allele frequency
      2. Population structure analysis
         1. AMOVA
         2. F-statistics
      3. Gene flow and migration patterns
         1. Isolation by distance
         2. Admixture events
      4. Genetic drift and natural selection
         1. Bottleneck effects
         2. Founder effects
      5. Coalescent theory
         1. Applications in genealogy
         2. Modeling demographic history
   5. Evolutionary Dynamics
      1. Speciation and hybridization
         1. Allopatric vs. sympatric speciation
         2. Introgression and hybrid zones
      2. Horizontal gene transfer
         1. Mechanisms and evolutionary implications
      3. Evolution of genetic systems
         1. Sex chromosome evolution
         2. Epigenetic inheritance
   6. Bioinformatics Tools for Evolution
      1. Software for phylogenetic analysis
         1. MEGA
         2. MrBayes
         3. RAxML
      2. Tools for population genetics
         1. PLINK
         2. Arlequin
      3. Databases for evolutionary data
         1. TreeBASE
         2. Dryad Digital Repository
   7. Case Studies in Evolutionary Bioinformatics
      1. Evolution of antibiotic resistance
      2. Speciation in island ecosystems
      3. Human evolution and migration patterns
   8. Challenges and Future Directions
      1. Integrating multi-omics data
      2. Dealing with incomplete lineage sorting
      3. Advances in statistical methods and computational power
      4. Contributions to conservation biology and biodiversity management