New: Annotation features available for Uniprot/SwissProt/PIR1 library searches.

FASTA Downloads

The source code for the FASTA programs is available from GitHub: branch v36.6.8
GitHub will always have the latest version of the FASTA code and the GitHub code will often be more current than the releases at the other sites (below).

Unix/MacOSX source code for the FASTA programs is available from

Versions of the program are in and


To run the FASTA programs on your own computers, you will need to (1) download and install the programs, and (2) download some databases to search.

Older versions - A quick guide the the current versions on the FASTA download site can be found here.

The current version of the FASTA programs is version 36, which includes fasta36, ssearch36, fastx/y36, tfastx/y36, prss36, prfx36, lalign36 etc. All of the fasta3 programs can be downloaded in a single file, either as Unix/MacOSX source code or as a Windows ZIP archive. (The fasta3.tar.gz and fasta3/windows/ files are the same as the files in the CURRENT directory.

Version 36 of the FASTA programs includes several major improvements: statistical estimates are much more accurate; threaded versions of the program are more efficient; and version 36 now includes lalign36, a program that finds multiple local alignments using Webb Miller's sim algorithm (and implementation of the Waterman and Eggert approach, PubMed) In addition, FASTAv36 includes ggsearch36 and glsearch36, which perform optimal global-global and global-local alignments and searches.

Older versions - In the past, a complete installation of the FASTA programs required downloading both the fasta3 and fasta2 programs, because some programs, notably lalign and align, were available only in fasta2. Now that lalign36 and ggsearch36 are available in the fasta3 package, there is much less reason to download fasta2. Nevertheless, the most recent version of the fasta2 programs can be downloaded as Unix/MacOSX source code or as a Windows ZIP archive

Downloading and Installing the FASTA3 programs

For Unix/Linux machines and Mac OSX, the FASTA source code file should be downloaded. Then:
  1. Uncompress and "un-tar" the fasta3.tar.gz file. At the Unix/Linux/MacOSX command line type: gunzip -c fasta3.tar.gz | tar xvf -

  2. The fasta36 distribution has Makefile's for most common architectures, including linux, Sun Solaris, MacOSX (both PowerPC and Intel), freebsd, IBM/Aix, etc. in the make/ directory. To see a list of the possible architectures, type (at the command line):
    ls -l make/Makefile.*

    Once you have identified a Makefile for your machine, e.g. linux64_sse2 (64-bit linux with SSE2), you will need to move to the src/ directory:
    cd src/
    and type:
    make -f ../make/Makefile.linux64_sse2 fasta36
    To compile just the fasta program or:
    make -f ../make/Makefile.linux64_sse2 all
    To compile all the programs. The program binaries are saved in the ../bin directory.

    You may encounter some warning messages, which can be ignored.

    Makefiles with sse2 (e.g. Makefile.linux32_sse2, Makefile.linux64_sse2, Makefile.os_x86, Makefile.os_x86_64) include an Intel SSE2 accelerated Smith-Waterman. These Smith-Waterman versions are typically more than 10-15X faster than unaccelerated versions, and can provide very fast sequence and profile Smith-Waterman searches. Makefile.os_x is designed for older G4/G5 Mac OS machines and provides an Altivec accelerated version of Smith-Waterman,

    In addition, makefiles that include sql in their name can be used to make versions of the programs that can read SQL databases directly.

  3. Once the programs are compiled, you can test whether fasta works by typing:
    ../bin/fasta36 -q ../seq/mgstm1.aa ../seq/prot_test.lseg
    which runs a test query sequence against a small test library.
  4. Once the programs are compiled, you may want to copy them to a more visible location, e.g. /usr/local/bin or /seqprg/bin. The easiest way to copy all the programs is to edit the Makefile you used and specify the executable directory in the line that starts: XDIR=/seqprg/bin. You can then type:
    make -f ../make/Makefile.linux64_sse2 install
    to install the programs, and make -f ../make/Makefile.linux clean-up to remove unnecessary files from the installation directory.

Downloading Sequence databases