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Initial version of phybema and first test data set
differences to Phybema as described in the B.Sc.-thesis of Birgitta P"auker: 1) use a python implementation of neighor joining. This saves system call since the neighbor-joining algorithm is called as a python function 2) conversion of output format is not necessary anymore. For all distance estimators we require that they output a matrix in phylip-format, either as a triangle or full matrix and with or without zero-values on the main diagonal
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- .gitignore 3 additions, 0 deletions.gitignore
- Makefile 7 additions, 0 deletionsMakefile
- README.md 1 addition, 1 deletionREADME.md
- src/PHYLIP_format_converter.py 116 additions, 0 deletionssrc/PHYLIP_format_converter.py
- src/calculate_ani.py 80 additions, 0 deletionssrc/calculate_ani.py
- src/callProg.py 73 additions, 0 deletionssrc/callProg.py
- src/callTreeCmp.py 75 additions, 0 deletionssrc/callTreeCmp.py
- src/concatFiles.py 39 additions, 0 deletionssrc/concatFiles.py
- src/create_dir.py 17 additions, 0 deletionssrc/create_dir.py
- src/dist_matrix.py 137 additions, 0 deletionssrc/dist_matrix.py
- src/estimators.py 114 additions, 0 deletionssrc/estimators.py
- src/ete.py 99 additions, 0 deletionssrc/ete.py
- src/nejo_idx.py 198 additions, 0 deletionssrc/nejo_idx.py
- src/openFile.py 18 additions, 0 deletionssrc/openFile.py
- src/parser.py 146 additions, 0 deletionssrc/parser.py
- src/phybema.py 202 additions, 0 deletionssrc/phybema.py
- src/print_comparison.py 139 additions, 0 deletionssrc/print_comparison.py
- src/root_dir.py 14 additions, 0 deletionssrc/root_dir.py
- src/test_requirements.py 51 additions, 0 deletionssrc/test_requirements.py
- src/write_time.py 37 additions, 0 deletionssrc/write_time.py
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