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revised README and added INSTALLATION

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1 parent 5e034f6 commit b47825f1aec3eab84b112016eb0cbf2da5e1c7d0 greg committed Jun 25, 2011
Showing with 27 additions and 3 deletions.
  2. +22 −3 README
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+Just a Makefile for now!
+Some of the programs are written in Haskell; you will need a Haskell
+compiler to build them. The Makefile currently expects ghc -
+you can obtain it from:
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+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 list of what they do:
-Various utilities for manipulating DNA sequence files in FASTA format.
-GCB 23feb11
+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:

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