This directory contains the source code for the FASTA package of programs, as well as executable binaries for the Windows32 and Mac OSX platforms.
The current major version of the FASTA programs is fasta36, which can be found in the fasta3 directory, the fasta36/ directory, and the CURRENT/ directory. fasta36 is a substantial improvement over fasta35, particularly because it displays multiple high-scoring local alignments (like BLAST HSPs), not just the best alignment. fasta36 is also faster, and provides much more accurate statistics for some scoring matrices. Older versions of the FASTA3 programs can be found in the fasta33-35 directory, and even older versions in the fasta2 directory.
Information on running the programs is available in doc/fasta_guide.pdf. Information on recent significant changes is available in changes_v36.html; minor version changes and bug fixes are documented in the doc/readme.v36 file.
The older FASTA2 package, which contains some "classic" programs for alignment, Kyte-Doolittle transmembrane prediction, and secondary structure prediction (chofas, garnier), is available in the fasta2 directory. The search and alignment programs in the fasta2 directory are out of date, and should not be used.
The (other/) directory provides other programs, including the nnnbat program for fitting DNA/RNA reassociation data (Pearson et al., 1977, Nuc. Acids Res. 4:1727-1737), and the GNJ program for building evolutionary trees (Pearson et al., 1999, Mol. Biol. Evol. 16:806-816).
The PUBS/ directory provides datasets and code from other publications, as does the data/ directory.
The near_optimal/ directory provides the programs described in Smoot et al., 2004, Bioinformatics 12:953-958.