1 | // ==================================================================== // |
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2 | // // |
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3 | // File : awt_parsimony_defaults.hxx // |
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4 | // Purpose : control behavior of parsimony // |
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5 | // // |
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6 | // // |
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7 | // Coded by Ralf Westram (coder@reallysoft.de) in July 2003 // |
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8 | // Copyright Department of Microbiology (Technical University Munich) // |
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9 | // // |
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10 | // Visit our web site at: http://www.arb-home.de/ // |
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11 | // // |
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12 | // // |
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13 | // ==================================================================== // |
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14 | |
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15 | #ifndef AWT_PARSIMONY_DEFAULTS_HXX |
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16 | #define AWT_PARSIMONY_DEFAULTS_HXX |
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17 | |
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18 | // -------------------------------------------------------------------------------- |
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19 | // Defines for PARSIMONY behavior |
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20 | |
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21 | // When MULTIPLE_GAPS_ARE_MULTIPLE_MUTATIONS is 'undefined' it compiles |
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22 | // an EXPERIMENTAL VERSION of parsimony that counts multiple |
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23 | // consequetive gaps as one mutation. |
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24 | // Our tests show that this method produces bad trees. |
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25 | // |
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26 | // Recommended setting is 'defined'. |
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27 | |
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28 | #define MULTIPLE_GAPS_ARE_MULTIPLE_MUTATIONS |
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29 | |
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30 | |
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31 | // When PROPAGATE_GAPS_UPWARDS is defined, gaps are propagates upwards |
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32 | // and they may match against gaps in neighbour sequences. |
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33 | // |
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34 | // Recommended setting is 'defined'. |
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35 | |
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36 | #define PROPAGATE_GAPS_UPWARDS |
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37 | |
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38 | // -------------------------------------------------------------------------------- |
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39 | // Do not change these settings! |
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40 | // -------------------------------------------------------------------------------- |
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41 | |
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42 | #else |
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43 | #error awt_parsimony_defaults.hxx included twice |
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44 | #endif // AWT_PARSIMONY_DEFAULTS_HXX |
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45 | |
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