comparison README.txt @ 4:4d47ab2b7bcc

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author davidmurphy
date Fri, 13 Jan 2012 07:18:19 -0500
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2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
3 logos from biological sequence alignments. It can be run on the command line,
4 as a standalone webserver or as a CGI webapp.
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7 For help on the command line interface run
8 ./codonlogo --help
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10 To build a simple logo run
11 ./codonlogo < cap.fa > logo.eps
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14 To run as a standalone webserver at localhost:8080
15 ./codonlogo --server
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18 An example file of probabilities is included, examplepriorfile.txt
19 It can be used with the following command.
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21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
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24 There is a known issue with GPL Ghostscript 9.04 which affects some users which may cause ghostscript to segfault.
25 This is not believed to be a problem with CodonLogo.
26 This is being investigated. if you encounter this problem it's recommended to downgrade to version 9.01 or earlier of ghostscript.
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30 -- Distribution and Modification --
31 This package is distributed under the new BSD Open Source License.
32 Please see the LICENSE.txt file for details on copyright and licensing.
33 The CodonLogo source code can be downloaded from
34 http://recode.ucc.ie/CodonLogo
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36 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
37 computational biology (http://code.google.com/p/corebio), and the python
38 array package 'numpy' (http://www.scipy.org/Download)