Mercurial > repos > davidmurphy > codonlogo
diff README.txt~ @ 8:5149eb3a89c2
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author | davidmurphy |
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date | Fri, 20 Jan 2012 09:03:40 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt~ Fri Jan 20 09:03:40 2012 -0500 @@ -0,0 +1,47 @@ + +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)