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6 days ago 7e6fb6e haoyu-haoyu:feat/clustalw-aln-format pull_requestCompare
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Comparefeat: add ClustalW .aln format support for sequence alignments
#880
haoyu-haoyu:feat/clustalw-aln-format
6 days ago
CPU Simulation
98 total
benchmark_score_threshold_rule[11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py2 s
benchmark_encode
benchmarks/sequence/benchmark_alphabet.py183.1 µs
benchmark_get_a3m_alignments
benchmarks/sequence/benchmark_fasta.py578.9 ms
benchmark_create_kmers
benchmarks/sequence/align/benchmark_kmer.py232.6 µs
benchmark_get_sequences[fasta_path0-NucleotideSequence]
benchmarks/sequence/benchmark_fasta.py183.9 ms
benchmark_get_sequences[fasta_path1-ProteinSequence]
benchmarks/sequence/benchmark_fasta.py8.8 ms
benchmark_indexing_from_kmer_selection[11*11*1*1***111-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py9.2 ms
benchmark_match_table[KmerTable-None]
benchmarks/sequence/align/benchmark_kmers.py15.2 ms
benchmark_match_table[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py15.2 ms
benchmark_similar_kmers
benchmarks/sequence/align/benchmark_kmer.py320.6 µs
benchmark_indexing_from_kmer_selection[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py12.3 ms
benchmark_structural_alphabet_methods[to_protein_blocks]
benchmarks/structure/benchmark_alphabet.py6.9 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py7.4 ms
benchmark_score_threshold_rule[None]
benchmarks/sequence/align/benchmark_kmers.py2 s
benchmark_clustering[upgma]
benchmarks/sequence/benchmark_phylo.py488.4 µs
test_pickle_and_unpickle[KmerTable-11*11*1*1***111]
benchmarks/sequence/align/benchmark_kmers.py38.9 ms
benchmark_indexing_from_kmer_selection[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py9.1 ms
benchmark_indexing_from_kmer_selection[None-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py12.3 ms
benchmark_structural_alphabet_methods[to_3di]
benchmarks/structure/benchmark_alphabet.py10 ms
benchmark_align_pairwise[align_banded]
benchmarks/sequence/align/benchmark_pairwise.py28.7 ms
benchmark_clustering[neighbor_joining]
benchmarks/sequence/benchmark_phylo.py626.6 µs
benchmark_indexing_from_sequences[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py17.6 ms
test_pickle_and_unpickle[BucketKmerTable(10000)-None]
benchmarks/sequence/align/benchmark_kmers.py7.4 ms
benchmark_indexing_from_kmers[None-BucketKmerTable(100000)]
benchmarks/sequence/align/benchmark_kmers.py10.1 ms
benchmark_indexing_from_kmers[11*11*1*1***111-KmerTable]
benchmarks/sequence/align/benchmark_kmers.py13.3 ms