File name: shm16_unix.tar.gz (300 kb) Brief description ----------------- Shm was designed to provide assistance in the analysis the distribution of somatic (point) mutations induced in the immunoglobulin genes of B- lymphocytes during the process of affinity maturation. This regulated process takes place in the germinal centres of the lymph nodes of superior vertebrates during an immune response directed against a 'foreign' antigen. It was shown that mutated immunoglobulin genes carried by the B cells in a given germinal centre can be clonally related. In order to emphasise such relationships among mutated genes attempts have been made at drawing clonal trees. However, in contrast to phylogenetic trees, the nodes in such clonal trees are sequences that are presently available rather than lost ancestors. To my knowledge, to date there is no software tool available that is suitable for the analysis of the distribution of somatic mutations in clonally derived B-lymphocytes. The shm program, available in versions for several processors and operating systems, builds clonal trees by a parsimony method and displays the trees of equal parsimony along with their distributions of somatic mutations. One can learn more about the basics of the somatic hypermutation process by reading any review article that deals with he subject (you may want to try to perform for this a Medline database search on http://www.ncbi.nlm.nih.gov/PubMed/medline.html by entering the keywords "somatic mutation" and "immunoglobulin"). Usage of these programs is free of charge. To download the shm package containing programs for Linux/i686 and SunOS: ------------------------------------------------------------------------ (1) Create a folder named SHM on your hard disk. (2) Change directory to folder SHM: cd SHM (3) Ftp shm16_unix.tar.Z onto your system in binary mode. (4) Uncompress it by typing: uncompress shm16_unix.tar.Z (5) Untar it by typing: tar -xvf shm16_unix.tar (6) Read the README file. There are also binary shm versions available for MS-Windows and MS-DOS. If you have problems or comments, please send e-mail to: cocea@necker.fr June 2, 1998 Laurentiu COCEA, M.D. M.Sc. Institut National de la Sante et de la Recherche Medicale Unite 373, 8e etage, porte 811Ter Faculte de Medecine Necker 156 rue de Vaugirard 75730 Paris Cedex 15, France tel: (+33) 14061 5384 fax: (+33) 14061 5590 cocea@necker.fr