** Changes with release 20u67 - May, 1999

Corrected serious problem with fastx alignments.

** Changes with release 20u66 - September, 1998

Made plalign, plfasta, psgrease, to be used with WWW pages.

plalign and plfasta now generate postscript graphics, rather
than tektronix graphics.  

psgrease makes postscript Kyte-Doolittle plots.

Provide various *.htm and *.cgi files to implement WWW pages for
lalign, plalign, grease, chofas, garnier.

Updated grease (tgrease), chofas, and garnier for consistent
user interface.

** Changes with release 20u65 - May 1998

Various minor bug-tweeks to the fastx function, faatran.c, and other
programs associated with fastx.

** Changes with release 20u64 - May, 1998

Programs have been modified to accept query sequences from STDIN for
WWW interfaces.  prss, prdf, lalign, and plalign should accept input
from STDIN. This makes it relatively easy to set up a prss WWW site.

The translation routine used by FASTX has been modified to translate
ambiguous nucleotides as 'X'.

Problems with specifying gap penalties with DNA sequences have been
corrected in prss.

**Changes with release 20u6 - August 1996

Another new program - TFASTX - compares a protein sequence to a
translated, potenitally frameshifted, DNA library.  TFASTX is a
substantial improvement over TFASTA, although TFASTX is slower.

The LALIGN/PLALIGN family now includes FLALIGN, which will write out
alignment plots in GCG's Figure format.

Mac - version now uses System7 Standard File routines.

BLOSUM62 support finally included.

** September, 1996

Fixed another bug in fastx/tfastx.

** September, 1996

Fixed problem with query subsequence selection.

Fixed problem with selectbestz().

** September 23, 1996

Fixed problem with in -m=10 Smith-Waterman alignments pointed
out and corrected by Erik Wallen (erikw@biokemi.su.se).

**Changes with release 20u61 - November, 1996

Made corrections to fffasta.c, nxgetaa.c to support alternative
protein scoring matrices with fastx.

**Changes with release 20u62 - December, 1996

A fix to nxgetaa.c to allow -i with fastx (bug caused by 20u61
changes).

**Changes with release 20u63 - December, 1996

Corrected some problems with lfasta using -m 10 (parseable) output.

**Changes with release 20u64 - September, 1997

Modified faatran.c so that fastx searches with many "X"'s are
translated to 'X', not 'K'.

Added -m 5 (MARKX), which combines -m 0 and -m 4.

Corrected problem with lalign/plalign/flalign and
lfasta/plfasta/flfasta when reverse complemented DNA sequences were
compared to the same file.


Bill Pearson
wrp@virginia.edu