Hello Everyone,
If we can let us start a thread that has all the recombination detection programs and algorithms with links and pros and cons. I'll start us off with the small list I have been working with.
Programs
RDP
Pros: Alread a compilation of detection algorithms for verification of analysis. Free and easy to install.
Cons: I can only get Manual methods to work on my Windows 7 machine specifically Bootscan, MaxChi, and 3Seq. Also poor interface.
SimPlot
Pros:Simple interface easy to use and visualize data. Implements algorithms Simplot, Bootscan, and FindSites.
Cons: Simplot More useful for evolutionarily closely related regions. Manual grouping of sequences in for analysis needs to be fixed. Can't seem to change window size or step size in Bootscan algorithm.
Algorithms
Bootscan
Pros: Works well with divergent sequences, very visual representation. Not only shows possible recombination but also can show you divergent regions in a proteins primary structure.
Cons: Not really sure how to best optimize parameters. Specifically for the more divergent sequences.
MaxChi
Pros: Easy to understand and optimize, visual representation
Cons: Seems like there is a higher false psotive rate when working with more divergent sequences
3Seq
Pros: Looks specifically at parental and recombinant sequences
Cons: Basically have no idea how this program works or what I should be looking for.
Simplot
Pros:Visual representation
Cons: Only works with highly similar sequences.
Anything you can add to thise would be greatly appreciated.
If we can let us start a thread that has all the recombination detection programs and algorithms with links and pros and cons. I'll start us off with the small list I have been working with.
Programs
RDP
Pros: Alread a compilation of detection algorithms for verification of analysis. Free and easy to install.
Cons: I can only get Manual methods to work on my Windows 7 machine specifically Bootscan, MaxChi, and 3Seq. Also poor interface.
SimPlot
Pros:Simple interface easy to use and visualize data. Implements algorithms Simplot, Bootscan, and FindSites.
Cons: Simplot More useful for evolutionarily closely related regions. Manual grouping of sequences in for analysis needs to be fixed. Can't seem to change window size or step size in Bootscan algorithm.
Algorithms
Bootscan
Pros: Works well with divergent sequences, very visual representation. Not only shows possible recombination but also can show you divergent regions in a proteins primary structure.
Cons: Not really sure how to best optimize parameters. Specifically for the more divergent sequences.
MaxChi
Pros: Easy to understand and optimize, visual representation
Cons: Seems like there is a higher false psotive rate when working with more divergent sequences
3Seq
Pros: Looks specifically at parental and recombinant sequences
Cons: Basically have no idea how this program works or what I should be looking for.
Simplot
Pros:Visual representation
Cons: Only works with highly similar sequences.
Anything you can add to thise would be greatly appreciated.
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