README.versions

May 13, 1997

Version overview

Currently, the fasta2u65.shar.Z is the latest complete fasta package,
and it has a complete set of searching programs (fasta, ssearch,
fastx, etc).  However, the searching programs are more in a maintenance
mode, bug fixes only.

The fasta3 series, which has ONLY the searching programs, has the
latest versions of the algorithms and statistical methods.  fasta3
also runs the exact same functions threaded (fasta3, fasta3_t) and in
parallel using PVM.

Here is a list of the programs, and where they can be found:

program		fasta2		fasta3			replaced by

fasta		yes		fasta3, fasta3_t

ssearch		yes		ssearch3, ssearch3_t

tfasta		yes		tfasta3, tfasta3_t	(tfastx3 preferred)

fastx		yes		fastx3, fastx3_t

tfastx		yes		tfastx3, tfastx3_t

rdf2 (obsolete)	no		no			prdf2

rss  (obsolete)	no		no			prss

prdf2		yes		no

prss		yes		no

lfasta		yes		no

lalign		yes		no

plalign		yes		no

flalign		yes		no

align		yes		no

align0		yes		no

randseq		yes		no

crandseq	yes		no

aacomp		yes		no

bestscor	yes		no

fromgb		yes		no

grease		yes		no

tgrease		yes		no

garnier		yes		no

zs_exp		yes		no