diff README.txt~ @ 8:5149eb3a89c2

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+
+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
+
+
+examplepriorfile contains the frequencies for codons in human CDS regions. 
+
+
+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.
+
+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)