File	Date	Author	Commit
.bzrignore	2011-10-19	Greg Benison	[da6157] added fastasel, select one of a series of records
.gitignore	2012-04-30	Greg Benison	[28d51f] added exclude information
AUTHORS	2011-06-25	greg	[5e034f] Added GPLv3 license
COPYING	2011-06-25	greg	[5e034f] Added GPLv3 license
INSTALLATION	2011-06-25	greg	[b47825] revised README and added INSTALLATION
Makefile	2011-10-19	Greg Benison	[da6157] added fastasel, select one of a series of records
README	2011-06-25	greg	[b07948] README: fix typo
TODO	2011-06-24	greg	[44550b] merge 'pipeline' branch
amplify	2012-01-10	Greg Benison	[49fce1] amplify: added debugging output option
fastacat.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastacomplement.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastacount.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastadigest.hs	2012-01-10	Greg Benison	[5c32e8] added ndeI
fastagap.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastahead.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastalint.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastamd5	2011-10-24	Greg Benison	[763783] added md5sum script
fastaorf.hs	2011-06-25	greg	[5e034f] Added GPLv3 license
fastasel.hs	2011-10-19	Greg Benison	[da6157] added fastasel, select one of a series of records
fastastack.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastatail.c	2011-06-25	greg	[5e034f] Added GPLv3 license
fastatranslate.hs	2011-06-25	greg	[5e034f] Added GPLv3 license
firstin.c	2011-06-25	greg	[5e034f] Added GPLv3 license
lexer.fl	2011-06-25	greg	[5e034f] Added GPLv3 license
pGFPe-Ler.fasta	2011-06-24	greg	[44550b] merge 'pipeline' branch
parameter.h	2011-06-24	greg	[44550b] merge 'pipeline' branch
seekable.c	2011-06-25	greg	[5e034f] Added GPLv3 license
subclone	2011-10-24	Greg Benison	[02555d] added 'subclone' script

Read Me

fasta-utils is a collection of command-line utilities for editing and
viewing DNA and protein sequences.  All fasta* programs take input
(from stdin) in FASTA format and many also produce output in FASTA
format, allowing them to be chained together with pipes.  Here is a
list of the programs and a short description of what they do:

fastacat             Catenate all sequences into one sequence
fastacomplement	     Replace each sequence with its reverse complement
fastacount	     Report sequence length
fastadigest	     Split sequences at restriction sites
fastagap	     Report positions of gaps in sequences
fastahead	     Echo only the first part of sequences
fastalint	     Reformat sequences to standard display width
fastaorf	     Find open reading frames
fastastack	     Interleave sequences for 'side-by-side' comparison
fastatail	     Drop the first 'n' bases
fastatranslate	     Convert DNA sequences to one-letter protein sequences     
amplify		     Predict PCR product from primers and template

The 'amplify' program for generating predicted PCR products is useful
for designing primers and cloning strategies and is an example of how
the core fasta* utilities can be combined using pipes for more complex
tasks.  It depends on the 'kalign' program, available at:
http://www.ebi.ac.uk/Tools/msa/kalign/