Recombination Detection Algorithms/Programs

[joshuapk]

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

http://darwin.uvigo.es/rdp/rdp.html

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
http://sray.med.som.jhmi.edu/SCRoftw...ot/#disclaimer
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

http://www.ncbi.nlm.nih.gov/pubmed/15665649

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

http://pubmlst.org/software/analysis/start/manual/max_chi_squared_test.shtml

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

http://bima.ws/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
http://sray.med.som.jhmi.edu/SCRoftw...lot/#geography
Pros:Visual representation
Cons: Only works with highly similar sequences.

Anything you can add to thise would be greatly appreciated.

[mbayer]

Hi,

there is also TOPALi v.2 (http://www.topali.org/). It's a Java based package, complete with a pretty fancy GUI, and it has an option for farming out some of the more computationally challenging tasks to our local compute cluster here, rather than making your own machine grind away for days.

Micha

[joshuapk]

Compatibility

I'll have to fight with it a bit to get it running since I am running Windows 7 64bit and 64bit JRE however thank you for the suggestion.

[anabio]

bratNextgen

http://www.helsinki.fi/bsg/software/BRAT-NextGen/

pros: highly cited, for microorganism
cons: need to instrall MCR first, encountered a problem, I've been fixing it... not successful yes..

[JackieBadger]

OmegaMap http://www.danielwilson.me.uk/omegaMap.html

[hpm]

"Links to Recombinant Sequence Analysis/Detection Programs" (http://bioinf.man.ac.uk/robertson/re...programs.shtml), might be helpful.

[sray]

Simplot - setting window and step sizes

At the top of this thread, @joshuapk said that s/he couldn't set the step and window sizes in Simplot. There are a couple of ways to do it, but the simplest is to click the value displayed (I think it's bottom-left) and you'll be prompted to modify it.

-- Stuart (author of Simplot)

Stuart C. Ray, M.D.
http://sray.med.som.jhmi.edu