Suggested topics for the CS 395T final project

You have at least two options for your final project. One is to do a project that involves software development, either to produce a new method and study it, or to compare existing methods. The other main option is to do a survey paper on some topic related to phylogenetic analysis and multiple sequence alignment. Of these two basic categories, the survey paper is much easier, but the first category is much more fun! So if you want to do a project that involves developing a new method or testing existing methods, please come see me early in the semester. I will help you learn how these studies are done, and we'll begin the planning for this kind of work early.

TREE RECONSTRUCTION

• Survey of Bayesian MCMC methods in phylogenetics for various kinds of data
• Supertree methods
• Supermatrix methods
• Missing Data - how handled, and what is the impact
• Fast evolving sites - detection, and then what?
• Models of evolution which aren't identifiable
• Computational complexity of maximum likelihood (theory)
• Heuristics for ML - how they *actually* operate

SITE VARIATION

• Heterotachy
• Covarion model
• Rates-across-sites (distributions and debates)
• Evidence (pro and con) regarding the molecular clock
• Deviation from the molecular clock (how defined, and how estimated)

ALIGNMENT

• Pairwise alignment of genomic sequences (allowing rearrangement events, duplications, etc.)
• Space-efficient algorithms
• Algorithms for (fixed tree) Tree Alignment - exact and approximate
• Gap penalty models (linear, affine, other)
• Models of evolution that incorporate indel events
• Generalized Tree Alignment algorithms and heuristics
• Techniques used for "cleaning up" the alignment

MISCELLANEOUS

• Rooting trees
• Software for simulation of evolution
• Gene Tree/Species Tree reconciliation
• Reticulation detection
• Inference of reticulation
• Models of speciation and "shape" effects
• The non-parametric bootstrap applied to large datasets
• The parametric bootstrap
• Phylogeny reconstruction on whole genomes, using gene order and content
• Reconstruction of ancestral states
• "Rogue taxa" identification
• Calculating evolutionary distances under conditions where the model formula cannot be applied

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