Another programme can count the variable sites, the informatives sites etc...
in a given alignement. it's MEGA which run on PCs.
10. MEGA (Molecular Evolutionary Genetic Analysis) is due to be released
at the beginning of 1993 by Sudhir Kumar, Koichiro Tamura, and Masatoshi Nei of
the Institute of Molecular Evolutionary Genetics, 328 Mueller Lab, Pennsylvania
State University, University Park, Pennsylvania 16802, U.S.A. It will be an
executable program for PCDOS machines, and will be menu-driven with context-
sensitive help. It will analyze data from DNA, RNA and protein sequences, and
distance matrices produced from other kinds of data as well. It will include
the Neighbor-Joining method distance matrix method, a branch and bound
parsimony method, and bootstrapping. It will also plot trees on many kinds of
printers. The program will be provided free of charge if you send one 1.2 Mb
5.25-inch or 1.44 Mb 3.5-inch floppy diskette, and will be sent as soon as it
is available. Inquiries can also be made by mail to M. Nei at the above
address or by electronic mail to nxm2 at psuvm (Bitnet) or nxm2 at psuvm.psu.edu