Team member: Irene Dhong Project Abstract: To study phylogeny, there are numerous methods, datasets, and analysis tools that aid in the study. In my project, I hope to survey several methods, datasets, and tools in order to identify stronger methods and runtime capabilities of tools in the process. Plan of Action: - Research numerous phylogeny program databases:
- Mainly - http://evolution.genetics.washington.edu/phylip/software.html
- Survey several different types of programs which require different datasets or implement the phylogeny in different methods.
- Method
- What will you implement
- Download the programs, run them on computer with associated datasets
- Make comparisons, based on accuracy, useability, effectiveness
- Take a look at source code to gage methods used to implement algorithm or what particular algorithm was used (ie. distance matrix)
- What methods are you going to compare and how will you get them?
- There are several different algorithms
- distance matrix
- parsimony
- general-purpose
- computation of likelihood
- Bayesian methods
- Which datasets are you going to use and where will you get them from (links if
possible)?
- Numerous datasets that are utilized in different programs
- microsatellite
- continuous quantative characters
- RAPDs, RFLPs, AFLPs
- What kind of experiment will you run and what will you measure (e.g., time, score, p-value etc).
- Compare phylogeny tools outputs - such as a visualization of the tree
- Compare program qualifications
- runtime
- datasets
- output quality
- effectiveness
Papers: www.cs.chalmers.se/~yehoshua/BayesSlides.pdf |
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