7-April-2024
This repository contains a slightly updated version of the fasta2.0 programs, which were last updated in May of 2006, but were not widely distributed after 2002, and not substantially modified after 1997.
This code should never be used for similarity searching research -- it has been entirely superceded by FASTA3, which is available from github.
The code has been made available for historical reasons, and to provide some very legacy non-FASTA programs:
- grease/psgrease (implementations of the Kyte-Doolittle algorithm)
- chofas (an implementation of the Chou-Fasman secondary structure prediction algorithm)
- garnier (an implementation of the Garnier secondary structure prediction algorithm)
The almost untouched fasta21u1d1 code from 2006 is in the initial version of this repository. This code runs, but does not produce the correct E()-values with gcc8.5 or clang, probably because of requirements to fully define arguments for external functions.
The current version of the code does compile and run, with many
warnings. I have tested fasta, fastx,lalign,grease,chofas,
and garnier and they seem to be working properly.
FASTA2 is a direct descendent of the first fasta described in
1988, when most personal computing was done with floppy disks. As a
result, it is very interactive, asking whether results should be saved
to a file, and how many results (and alignments) should be displayed.
To get a more modern experience, run it with the -q (quiet)
option. It will then run from command line arguments like the current
version of fasta.
These programs compile without errors with clang (Mac OSX) using:
make
Getting the source code to this state required extensive editing to define functions appropriately, but no changes were made to the actual algorithms used (the compilers picked up a few format string errors that were corrected). While the programs compile without errors, there are many warnings.
There is also a lot of excess #defines/code to accomodate the compilers that where available when this code was was distributed (particularly MetroWerks 'C' under the Mac System.X OS). Those defines have not been touched, but the code has only been tested under MacOS and Linux.
Bill Pearson wrp@virginia.edu