Antigen Receptor Diversity
ARPP UAI is the latest in a series of programs for the inference of antigen receptor rearrangements. ARPP UAI was developed to provide an estimate of the posterior probability over unmutated ancestors, and to use either single immunoglobulin polynucleotide sequences or alignments of clonally related immunoglobulin sequences.
SoDA (Somatic Diversification Analysis) and SoDA2 are programs provided for the inference of immunoglobulin and T-cell receptor rearrangements. SoDA2 (temporarily unavailable) uses a hidden Markov model for CDR3 of human immunoglobulin genes. It is the more recent of the two programs, and is preferred over SoDA for human immunoglobulin genes. SoDA one uses a multidimensional dynamic programming, and works with both immunoglobulins and T-cell receptors in mouse, human, rhesus macaque (Macaca mulatta) and opossum (Monodelphis domestica).