README.TXT BRIEF EXPLANATIONS OF FILES ON
DISK SNEATH_ST1
There are the following files:
README.TXT This file.
phs5t14.bas Program (GWBASIC or QBASIC) to screen a
matrix of molecular sequences for atypical
sequence comparisons using a modified
Sherman statistic.
The program can be used
on either nucleotide or protein sequences,
and compares all the t(t-1)/2 comparisons
for t sequences. It prints the Sherman
statistic w and also functions of it,
including the normal standard error score z,
the corresponding normal probability P,
and for convenience, -2 ln P which is useful
for some statistical purposes.
The program also gives several
summaries of the results for individual
sequences and the distances between sequences.
phs5t14c.bas A version of phs5t14.bas which corrects for
the constant-site effect for the three codon
positions.
phs6t06.bas Program (GWBASIC or QBASIC) to simulate the
addition of constant sites to randomly-placed
differences in a molecular sequence comparison.
This sequence consists of similarities, S, and
differences, D, and uses the modified Sherman
statistic. The output gives the values of
w and some derivatives for various values of
the number off added constant sites, c.
5t14a.dat A file of test data with a recombinant sequence,
so as to obtain a high probability for one
comparison, and including numbers of constant
sites as a final row. To be copied
to file phs5t14.dat which is the input file
for programs phs5t14.bas and phs5t14c.bas.
NOTE THAT THIS WILL OVERWRITE THE
PREVIOUS phs5t14.dat; therefore do not rename
any files, but copy them; the originals will
then be unchanged.
5t14b.dat A small test file to copy to phs5t14.dat.
5t14c.dat Another small test file to be copied to
phs5t14.dat.
pimelmt.dat A nucleotide matrix of mitochondria of
Pimelia beetles, for full testing of programs
phs5t14.bas and phs5t14c.bas after it has been
copied to phs5t14.dat.
Cheers, Michael.
Michael J. Sackin, Senior Computer Officer, Dept of Microbiology &
Immunology, University of Leicester, PO Box 138, University Road,
Leicester LE1 9HN, UK email: mjs@le.ac.uk
Phone: (+44) 116-252 2957 FAX: (+44) 116-252 5030