--- a/README.txt	Mon Jan 16 07:03:36 2012 -0500
+++ b/README.txt	Fri Jan 20 09:03:40 2012 -0500
@@ -1,38 +1,51 @@
-
-CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 
-logos from biological sequence alignments.  It can be run on the command line,
-as a standalone webserver or as a CGI webapp.
-
-
-For help on the command line interface run
-    ./codonlogo --help
-
-To build a simple logo run
-    ./codonlogo  < cap.fa > logo.eps
-
-
-To run as a standalone webserver at localhost:8080 
-    ./codonlogo --server
-
-
-An example file of probabilities is included, examplepriorfile.txt
-It can be used with the following command.
-
-    ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
-
-
-There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault. 
-This is not believed to be a problem with CodonLogo.
-This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
-
-
-
--- Distribution and Modification --
-This package is distributed under the new BSD Open Source License. 
-Please see the LICENSE.txt file for details on copyright and licensing.
-The CodonLogo source code can be downloaded from 
-http://recode.ucc.ie/CodonLogo
-
-CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
-computational biology (http://code.google.com/p/corebio), and the python
-array package 'numpy' (http://www.scipy.org/Download)
+
+CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence 
+logos from biological sequence alignments.  It can be run from the command line as a standalone webserver or as a CGI webapp.
+
+
+For help on the command line interface run
+    ./codonlogo --help
+
+To build a simple logo run
+    ./codonlogo  < cap.fa > logo.eps
+
+
+To run as a standalone webserver at localhost:8080 
+    ./codonlogo --server
+
+
+An example file of probabilities is included, examplepriorfile.txt
+It can be used with the following command.
+
+    ./codonlogo --prior ./examples/Escherichiacoli.txt < cap.fa > logo.eps
+
+
+examplepriorfile contains the frequencies for codons in human CDS regions. 
+
+
+KNOWN ISSUES:
+
+There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault or prevent codonlogos from being generated in anything other than eps format. 
+
+This is believed to be an issue with ghostscript and a bug report has been submitted to the ghostscript mailing list.
+This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 of ghostscript or earlier .
+
+
+
+For converting files to a suitable format the following sites can be used:
+
+http://genome.nci.nih.gov/tools/reformat.html
+http://www-bimas.cit.nih.gov/molbio/readseq/
+
+
+
+
+-- Distribution and Modification --
+This package is distributed under the new BSD Open Source License. 
+Please see the LICENSE.txt file for details on copyright and licensing.
+The CodonLogo source code can be downloaded from 
+http://recode.ucc.ie/CodonLogo
+
+CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
+computational biology (http://code.google.com/p/corebio), and the python
+array package 'numpy' (http://www.scipy.org/Download)