QuasiRecomb

Developer's DescriptionBy Armin TopferGenerate and analyze viral Quasispecies subjected to recombination.QuasiRecomb is a lightweight application that runs in the command console, simulating a Markov model for generating viral Quasispecies. It describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and tested by applying to reads obtained from experimental HIV samples. It offers an implementation of the EM algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies.