Evolutionary Analysis of Protein families
- Weighted sum of pairs scoring for multiple sequence alignment
- Codon bias
- Ancestral Sequence Reconstruction
- Molecular Dating
Problem: SynPAM appears to be useful as a tool for molecular dating.
We need to verify and compare it to existing methods.
Run simulations and use real data to compare SynPAM, dS, Ks,
- Methods for comparing likelihood models
- Dependence of the TSP performane on topology
Using a circular tour order to construct and score multiple sequence alignments
has been shown to improve the resulting alignments. However, the topology of the
phylogenetic tree describing the evolution of the sequences being aligned can
affect the ability of the circular tour to improve the results.
This work is to investigate the dependence of the circular tour on tree
topology using real and simulated multiple sequence alignments and trees.
As circular tours are found via the travelling salesman problem, this is
an investigation of the dependence of the results of the TSP algorithm
on the spacing of the cities.
Practically, the student would be expected to use existing implementations of
the TSP to analyze real and simulated data (real alignments exist, a simulation
platform must be implemented by the student) to find if and under what
circumstances the circular tour fails. The results of these analyses
will possibly be used to improve the TSP implementation. The programming
language is Darwin, an interpreted language very similar to Maple.
- SynPAM Validation- Barbara Keller
- A model of transposon evolution- Florian Walpan
- Evolution of the tRNA Pairing Index- Michel Guex
- A Protein Visualization Tool- Farid Dshabarow
- Joint reconstruction of Phylogenetic Trees with Rate Variation- Yves Jacoby
- Stock Market Simulation based on Black-Box Models- Patric Somlo
- Framework for simulation and evaluation of algorithmic trading in a distributed environment- Marcus Deluigi
- Genome Clustering in order to accelerate multiple genome comparison- Benjamin Schaller
- Finding a maximum Almost-clique- Hansruedi Peter
- Local effect of codon bias on secondary structural units of the proteins in S. cerevisiae- Anh-Thu Tieu
- Codon Mutation Matrices- Adrian Schneider link
- SynPAM- a measure of synonymous distance- Adrian Schneider link
- Phylogenetic Tree Construction using Gaps Victor Goetsch
- Structure Prediction of Pseudomonas putida Alkane Hydroxylase by means of Compensatory Covariation Analysis- Franz Roos
- Phylogentic Tree Construction via Genetic Algorithms