Constructed Neighbour net using Split Tree v. 4 with concatenate sequence of few genes from my bacteria under study. Please make me understand how to infer recombination events.
SplitsTree is good for showing you soemthing about how much recombination has happened, and a little bit about which "species" or "OTUs" were involved in exchanging DNA between them. But it does not tell you anything about which genes or gene regions were exchanged, or the direction of transfer, or other details. If you see from SplitsTree that there is recombination or DNA exchange happening in your data set, you then can move on to programs such as SimPlot or build trees with individual genes or gene regions to further explore which DNA was exchanged between species or isolates.
https://sray.med.som.jhmi.edu/SCRoftware/simplot/
SimPlot would be appropriate for a few genes from several or many species, but is not really designed for a huge data set like complete bacterial genomes. But there are other programs to help with very large data sets.
I am attaching a sample SimPlot, illustrating that there is a lineage of HIV-1 named "Circulating Recombinant Form 03_AB" which is recombinant between HIV-1 subtype A highlighted in green, and HIV-1 subtype B highlighted in red. The blue is other isolates of the CRF03_AB form of the virus, showing that this was one recombination event followed by diversification of the recombinant lineage and not different recombination events between A and B viruses resulting in similar A/B recombinants.
- Badges
- Science method