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enable pairwise sequence alignments with parasail
Parasail: https://github.com/jeffdaily/parasail It's faster than the pairwise sequence algorithms we have in OpenStructure. However, the main reason to check out another solution is the fact that OpenStructure may return suboptimal alignment results. This is a result of how the dynamic programming table is built. If for a certain cell in the dynamic programming table a match state and insertion state score equally, match is preferred. There is a chance that we would get a better score later on if we would stick with the insertion state (gap open penalties vs. gap extension penalties). Not sure if this will be fixed in the near future.
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- CMakeLists.txt 12 additions, 1 deletionCMakeLists.txt
- cmake_support/FindParasail.cmake 11 additions, 0 deletionscmake_support/FindParasail.cmake
- modules/bindings/doc/bindings.rst 1 addition, 0 deletionsmodules/bindings/doc/bindings.rst
- modules/bindings/doc/parasail.rst 74 additions, 0 deletionsmodules/bindings/doc/parasail.rst
- modules/bindings/pymod/CMakeLists.txt 1 addition, 0 deletionsmodules/bindings/pymod/CMakeLists.txt
- modules/bindings/pymod/export_parasail.cc 42 additions, 0 deletionsmodules/bindings/pymod/export_parasail.cc
- modules/bindings/pymod/wrap_bindings.cc 2 additions, 0 deletionsmodules/bindings/pymod/wrap_bindings.cc
- modules/bindings/src/CMakeLists.txt 5 additions, 3 deletionsmodules/bindings/src/CMakeLists.txt
- modules/bindings/src/wrap_parasail.cc 195 additions, 0 deletionsmodules/bindings/src/wrap_parasail.cc
- modules/bindings/src/wrap_parasail.hh 49 additions, 0 deletionsmodules/bindings/src/wrap_parasail.hh
- modules/config/CMakeLists.txt 5 additions, 0 deletionsmodules/config/CMakeLists.txt
- modules/config/config.hh.in 1 addition, 0 deletionsmodules/config/config.hh.in
- modules/doc/install.rst 12 additions, 0 deletionsmodules/doc/install.rst
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