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4
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1
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2 CodonLogo (http://recode.ucc.ie/CodonLogo) is a tool for creating sequence
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3 logos from biological sequence alignments. It can be run on the command line,
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4 as a standalone webserver or as a CGI webapp.
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5
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6
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7 For help on the command line interface run
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8 ./codonlogo --help
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9
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10 To build a simple logo run
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11 ./codonlogo < cap.fa > logo.eps
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12
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13
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14 To run as a standalone webserver at localhost:8080
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15 ./codonlogo --server
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16
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17
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18 An example file of probabilities is included, examplepriorfile.txt
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19 It can be used with the following command.
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20
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21 ./codonlogo --prior examplepriorfile.txt < cap.fa > logo.eps
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22
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23
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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.
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25 This is not believed to be a problem with CodonLogo.
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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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27
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28
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29
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30 -- Distribution and Modification --
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31 This package is distributed under the new BSD Open Source License.
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32 Please see the LICENSE.txt file for details on copyright and licensing.
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33 The CodonLogo source code can be downloaded from
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34 http://recode.ucc.ie/CodonLogo
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35
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36 CodonLogo requires Python 2.6 or 2.7, the corebio python toolkit for
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37 computational biology (http://code.google.com/p/corebio), and the python
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38 array package 'numpy' (http://www.scipy.org/Download)
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