** January, 2007

Modify align.c (used for global alignments) to use the same scoring matrices, and other options, as lalign2.c.

Makefile has been modified so that make all only makes FASTA2 programs
that are not part of FASTA3.  The search programs are no longer made
by default.

** December, 2006

Modify fffasta.c to support the **pam2 global in upam.gbl, rather than
pam2[][] - **pam2 was introduced for lalign2.c/lsim3.c.

** August, October 2006, 21u08 (lalign2.c)

Make some efforts to remove global variables from lsim2.c, by
replacing it with lsim3.c.  Initial efforts in August, 2006,
introduced a bug, which was detected and fixed in October.

Provide option to show identical alignments.

** May, 2005,  21u07 (lalign.c)

Modify the code that checks for identical sequences to not assume
sequences are identical just because the filenames are.  They may
be different because of sub-setting.

Add -I option to show identical alignment.

Update lalign.1 documentation.

** April, 2004, 21u06 (lalign2.c)

Fix problem reading external scoring matrix files.  The file
was not read, and then sequences were not read properly.

Incorporate GAP_OPEN gap matrix options.

Changes to allow G:U RNA base matches.

** March, 2000, 21u02 (lalign.c) 

Added '-N length' option to limit query, library sequences to
"length".  Corrected problems with sequence numbering when
subsequences were specified.

Modifications to nrand.c to keep more bits and return random numbers
from 0..n-1.  Use "nrandom.c" rather than nrand.c if random() is
available.

Fixes to shuffling routines in randlib.c.

** November, 2003

Add Blosum80 matrix to lalign.c, upam.gbl.