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