4 The latest versions of the FASTA search programs are in fasta3.shar.Z.
5 This file contains the fasta34 series of programs. fasta34 also runs
6 the exact same functions threaded (fasta33, fasta33_t) and in parallel
9 Here is a list of the programs, and where they can be found:
11 program fasta2 fasta34 replaced by
13 fasta yes fasta34, fasta34_t
15 ssearch yes ssearch34, ssearch34_t
17 tfasta yes tfasta34, tfasta34_t (tfastx34 preferred)
19 fastx yes fastx34, fastx34_t
20 fasty no fasty34, fasty34_t
22 tfastx yes tfastx34, tfastx34_t
23 tfasty no tfasty34, tfasty34_t
25 fasts/tfasts no fasts34(_t), tfasts34(_t)
27 fastf/tfastf no fastf34(_t), tfastf34(_t)
35 The following programs are part of the fasta2 program package. The
36 latest version of fasta2 is fasta20u66.shar.Z.
38 The most useful fasta2 programs are lalign and plalign, which calculate
39 multiple non-intersecting local alignments using Webb Miller's "sim"
40 implementation of the Waterman-Eggert algorithm.
42 You should not use the fasta2 programs for library searching; the
43 fasta3 programs are more sensitive and have better statistics.
73 The fasta3.shar.Z and fasta2.shar.Z files a Unix "shell archive" files.
74 To unpack them, go into an empty directory and type:
76 zcat fasta3.shar.Z | sh
78 You can then make the programs by typing:
82 Makefile's are available for many platforms, e.g.
84 make -f Makefile.linux
87 etc. You are much better off using the pre-configured Makefile.???
88 than trying to edit the Makefile (which is designed for a Compaq/HP
91 Precompiled versions of the programs for Mac and Windows are available
92 in the mac_fasta and win32_fasta directories. If you are running
93 MacOSX from the command line, use the Unix version (fasta3.shar.Z and