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subtitution matrices: Add string identifier and remove MATCH and IDENTITY presets
The reason for removing MATCH and IDENTITY is to only have matrices which are also available in the parasail library. This simplifies the usage of parasail as a drop-in replacement. To be honest: I doubt that anyone used these matrices.
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- modules/seq/alg/doc/seqalg.rst 52 additions, 9 deletionsmodules/seq/alg/doc/seqalg.rst
- modules/seq/alg/pymod/mat.py 1 addition, 4 deletionsmodules/seq/alg/pymod/mat.py
- modules/seq/alg/pymod/wrap_seq_alg.cc 3 additions, 2 deletionsmodules/seq/alg/pymod/wrap_seq_alg.cc
- modules/seq/alg/src/subst_weight_matrix.cc 5 additions, 31 deletionsmodules/seq/alg/src/subst_weight_matrix.cc
- modules/seq/alg/src/subst_weight_matrix.hh 7 additions, 3 deletionsmodules/seq/alg/src/subst_weight_matrix.hh
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