| /dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/ |
| H A D | score.py | 16 …def __init__(self, gap_open, gap_extend, default=-100, alphabet1="ACGT", alphabet2=None, gap1="-",… argument
125 def read_scoring_scheme(f, gap_open, gap_extend, gap1="-", gap2=None, **kwargs): argument
140 def build_scoring_scheme(s, gap_open, gap_extend, gap1="-", gap2=None, **kwargs): argument
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| /dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Matrix/ |
| H A D | Mlagan.pm | 121 sub gap_open { subroutine
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| /dports/biology/fasta3/fasta-36.3.8/src/ |
| H A D | smith_waterman_sse2.c | 36 unsigned short gap_open, in smith_waterman_sse2_word()
233 unsigned char gap_open, in smith_waterman_sse2_byte()
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| H A D | smith_waterman_altivec.c | 29 unsigned short gap_open, in smith_waterman_altivec_word()
1069 unsigned char gap_open, in smith_waterman_altivec_byte()
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/core/ |
| H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly()
166 Int4 gap_open, Int4 gap_extend, in s_NuclSmithWaterman()
280 Int4 gap_open, Int4 gap_extend, in s_GetTraceback()
441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local
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| H A D | hspfilter_mapper.h | 53 Int4 gap_open; member
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/core/ |
| H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly()
166 Int4 gap_open, Int4 gap_extend, in s_NuclSmithWaterman()
280 Int4 gap_open, Int4 gap_extend, in s_GetTraceback()
441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/core/ |
| H A D | blast_sw.c | 59 Int4 gap_open, Int4 gap_extend, in s_SmithWatermanScoreOnly()
166 Int4 gap_open, Int4 gap_extend, in s_NuclSmithWaterman()
280 Int4 gap_open, Int4 gap_extend, in s_GetTraceback()
441 Int4 gap_open = score_params->gap_open; in SmithWatermanScoreWithTraceback() local
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| /dports/biology/ncbi-toolkit/ncbi/algo/blast/api/ |
| H A D | blast_options_api.c | 212 Int4 gap_open, Int4 gap_extend) in SBlastOptionsSetMatrixAndGapCosts()
248 Int4 gap_open, Int4 gap_extend, in SBlastOptionsSetRewardPenaltyAndGapCosts()
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| /dports/biology/seqan1/seqan-1.3.1/seqan/blast/ |
| H A D | blast_report.h | 83 float gap_open; variable
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| /dports/biology/diamond/diamond-2.0.13/src/stats/ |
| H A D | score_matrix.cpp | 40 ScoreMatrix::ScoreMatrix(const string & matrix, int gap_open, int gap_extend, int frameshift, int s… in ScoreMatrix()
150 ScoreMatrix::ScoreMatrix(const string& matrix_file, int gap_open, int gap_extend, int stop_match_sc… in ScoreMatrix()
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| /dports/biology/wise/wise2.4.1/src/models/ |
| H A D | lba.c | 54 Probability gap_open = 0.1; in main() local
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| /dports/biology/diamond/diamond-2.0.13/src/tools/ |
| H A D | benchmark_swipe.cpp | 33 Sv scores, gap_extension, gap_open, best; in update_row() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/algo/blast/api/ |
| H A D | rps_aux.cpp | 96 int gap_open, in CBlastRPSAuxInfo()
199 int gap_open; in x_ReadFromFile() local
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/blast/api/ |
| H A D | rps_aux.cpp | 96 int gap_open, in CBlastRPSAuxInfo()
199 int gap_open; in x_ReadFromFile() local
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| /dports/biology/mmseqs2/MMseqs2-13-45111/src/test/ |
| H A D | TestAlignmentPerformance.cpp | 82 int gap_open = 10; in main() local
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| H A D | TestProfileAlignment.cpp | 795 int gap_open = 10; in main() local
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| H A D | TestAlignment.cpp | 85 int gap_open = 11; in main() local
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| /dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/algo/blast/core/ |
| H A D | hspfilter_mapper.h | 53 Int4 gap_open; member
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/blast/core/ |
| H A D | hspfilter_mapper.h | 53 Int4 gap_open; member
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| /dports/biology/diamond/diamond-2.0.13/src/output/ |
| H A D | xml_format.cpp | 80 void XML_format::print_header(Consumer& f, int mode, const char* matrix, int gap_open, int gap_exte… in print_header()
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| H A D | sam_format.cpp | 125 void Sam_format::print_header(Consumer &f, int mode, const char *matrix, int gap_open, int gap_exte… in print_header()
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| H A D | blast_pairwise_format.cpp | 85 void Pairwise_format::print_header(Consumer &f, int mode, const char *matrix, int gap_open, int gap… in print_header()
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| /dports/biology/exonerate/exonerate-2.4.0/src/model/ |
| H A D | affine.h | 28 C4_Score gap_open; member
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| /dports/biology/ugene/ugene-40.1/src/libs_3rdparty/samtools/src/samtools/ |
| H A D | kaln.h | 34 int gap_open; member
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