Reconstructing a B-cell clonal lineage: Antigen Receptor Probabilistic Parser (ARPP) software and Clone K/H FASTA files

These files are supplementary to the paper “Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors”, which describes the inference of the unmutated ancestor to a set of clonally related antibody genes. The software that implements the methods described is called ARPP UAI, for antigen receptor probabilistic parser: unmutated ancestor inference.

setup.exe is the installer for ARPP UAI. Double click the icon, and follow the steps as indicated in the installation wizard. It will install the program and create an icon on your desktop. The program requires a windows operating system to run.

ARPP QuickStart is a very brief manual describing how to run the program and interpret its output.

CL558(CloneK).fasta and GenbankIgHC2(CloneH).fasta are data input files that can be used to test the installation. These are the datasets that were used to generate the results in the paper. The first of these is a small clone of human kappa sequences, called Clone K in the paper. The latter is a large clone of human heavy chain sequences, called Clone H in the paper.