30 July 1997

Recommend blosum62 matrix with gap penalty of 12 and no constant.
In tests, this gives better alignments than the old defaults.

Changes to randomisation routines.  Dump the Numerical recipes 
routines and use the system supplied routines.  Note:  this
has only been tested on Silicon Graphics under IRIX 5.3 and 6.2.




30 March 1994

Fix bug in ORDER.  This had the effect of producing strange
trees in Postscript output.  It also caused crashes on some
platforms (e.g. ALPHA OSF/1).  This was simply a format statement
that was differently interpreted by the MIPS compiler.

Added Makefiles and BUILD option for DEC alpha/osf1.  The makefiles
are basically the same as those for Silicon Graphics.  I have not 
experimented with the optimizer flags on the alpha/osf1.  (Note:
the OSF1 port was done while visiting another lab - I don't have such
a machine so can't check out problems you may have with this 
version).

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