Virus Recombination Analysis¶
更新于: 2020-09-14
常见的病毒重组分析软件¶
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: 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...red_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.
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..
OmegaMap http://www.danielwilson.me.uk/omegaMap.html TOPALi v.2 (http://www.topali.org/).
http://bioinf.man.ac.uk/robertson/recombination/programs.shtml