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[jabaws.git] / website / archive / binaries / mac / src / fasta34 / readme.w32

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-October 6, 2006
-
-The FASTA programs for Windows32 environments (WindowsNT, 2000, XP)
-has undergone a major upgrade, so that now all the programs in the
-Unix/MacOSX distribution are available to Windows users.  Moreover,
-Windows users with modern (SSE2 compatible) processors can run greatly
-accelerated versions of the Smith-Waterman ssearch program.
-
-Moreover, these programs work both with FASTA formatted files, and
-NCBI BLAST formatted files.
-
-The following programs are available:
-
-    fasta34.exe                protein-protein or DNA-DNA database searches
-    fastf34.exe
-    fastm34.exe
-    fasts34.exe
-    fastx34.exe                compare DNA query to protein library with frameshifts
-    fasty34.exe                compare DNA query to protein library with frameshifts
-    prfx34.exe
-    prss34.exe         evaluate statistical significance using shuffles
-    prss34sse2.exe
-    ssearch34.exe      Smith-Waterman for prot-prot or DNA-DNA searches
-    ssearch34sse2.exe  Smith-Waterman, accelerated with SSE2 extensions
-    tfastf34.exe
-    tfastm34.exe
-    tfasts34.exe
-    tfastx34.exe       compare protein to DNA library with frameshifts
-    tfasty34.exe       compare protein to DNA library with frameshifts
-
-Each of these programs also has a "threaded" version, which can run on
-multiple processors (or dual cores) if they are available.  However,
-they are built using the Unix pthreads API, so to use these programs,
-you must download the pthreadVC2.dll from:
-
-ftp://sources.redhat.com/pub/pthreads-win32/dll-latest/lib/pthreadVC2.dll
-
-see also http://sourceware.org/pthreads-win32/
-
-    fasta34_t.exe
-    fastf34_t.exe
-    fastm34_t.exe
-    fasts34_t.exe
-    fastx34_t.exe
-    fasty34_t.exe
-    prfx34_t.exe
-    prss34_t.exe
-    prss34sse2_t.exe
-    ssearch34_t.exe
-    ssearch34sse2_t.exe
-    tfastf34_t.exe
-    tfasts34_t.exe
-    tfastx34_t.exe
-    tfasty34_t.exe
-
-Without that DLL, the threaded programs will not run at all. The
-current compilation supports two threads, and speeds up searches about
-2-fold on dual-core processors.
-
-The programs have been tested with protein and DNA databases in FASTA
-format, PIR/GCG-text format, and Genbank flatfile format.  The program
-does not work properly with GCG binary format databases, but it seems
-unlikely that Windows users would need these. 
-
-Be certain to use an program that can work with long file names when
-unpacking the program source files.
-
-Please report bugs to:
-
-       wrp@virginia.edu