Enables the simulation of time-resolved antibody repertoires. AbSim is an R package that allows user to comprehensively control the vast biologically-relevant parameter space of antibody repertoire selection and evolution. The control of the following parameters is possible by: (i) total time of evolution, (ii) rate and method of somatic hypermutation (SHM), (iii) number and rate of recombination events, (iv) rate at which new sequences are produced, (v) baseline mutation rate, (vi) clonal frequency, and (vii) germline gene usage distribution.
Calculates the probability of generating a given CDR3 amino acid sequence or motif. OLGA implements an exact computation of the generation probability of any B-cell receptor (BCR) or T-cell receptor (TCR) sequence or motif. The software can compute the probabilities of CDR3 sequences and motifs, with or without V/J restriction, of 4 chain loci, but the list can be expanded. It can serve to compute baseline receptor frequencies and to identify outlying sequences in repertoire sequencing datasets.
Simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools. IgSimulator tool addresses various complications in generating realistic antibody repertoires. IgSimulator’s code has modular structure and can be easily adapted to new requirements to simulation.