Enclosed is a new release of FASTA for the Macintosh - version 2.0x2
(July, 1995).  This version has a number of major improvements over
previous versions of FASTA, some of which are documented below.  In
addition, this is the first version with a PowerPC implementation.  If
you have a PowerPC Mac, be sure to run the fasta.ppc program, rather
than fasta.68k.  Users with 68K (68020,68030,68040) Mac's must use the
fasta.68k versions.

The latest versions of FASTA are all available via anonymous FTP
from ftp.virginia.edu in pub/fasta (/mac, /dos).

Currently, there is no written documentation for this version of
MacFASTA.  However, the file "fasta20.doc" in the "docs" folder
provides complete documentation for this version.

Bill Pearson, July, 1995
_________________________________________________________
 
Because of the large number of programs, this release has been provided
as a self-extracting Compactor-Pro archive.  To install:

          1) Create a new folder on your hard disk:  fasta2.0x

          2) double-click the fasta20x.cpe icon.

          3) double-click the file "fastgbs" and edit it to reflect the
location of the sequence libaries on your machine. For example, if you
keep the PIR protein sequence database in a folder on
"HD80:SEQUENCE:PIR:", you should change the entry that reads:
"WRPMAC:SLIB:" to "HD80:SEQUENCE:PIR". As you edit the "fastgbs" file,
make certain that any files of file names, e.g. "pir.nam", are also
modified to point to the correct sequence library folder.

          4) Drag all of the sequences in the "sequences" folder to the
main "fasta2.0" folder.   For reasons that I do not understand, fasta and
tfasta do not find library sequences in the "sequences" folder (align,
lalgin, lfasta, plfasta, etc. seem to work properly).

           5) test fasta by double clicking the "fasta" application icon
and type:

                musplfm.aa lcbo.aa

on the command line.


Good luck.   Please inform me a bugs, as this is a new release of a major
revision.

Bill Pearson wrp@virginia.EDU

______________________________________________________________
Changes with 2.0x  (March, 1995)

	Change default protein matrix to BLOSUM50.  PAM250 is
	still available with -s 250.  Change program to accept gap
	penalties from the command line with "-f" (-12) and "-g" (-2).

	Provide MARKX=4, which allows one to display the conserved
	regions of the query sequence after a library search.

	Calculate explicit probability estimates for FASTA, TFASTA,
	and SSEARCH.  Estimates assume that the library contains a large
	number of unrelated sequences.  If this is not correct, the
	estimates are useless (and should be turned off with the -z
	flag).

	The width of the band used to calculate optimized scores is
	now variable.  For proteins and ktup=1, 32 residues are used,
	otherwise 16 residues are used.  For DNA, 16 residues are
	used. This value can be changed with the "-y" option.

	FASTA alignments now use the Smith-Waterman algorithm and are
	not limited by the number of gaps.