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v0.7.0

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@brendanf brendanf released this 22 Aug 15:21
· 171 commits to master since this release
  • Introduce functions to calculate pairwise distances and output a distance
    matrix. These use edlib and WFA2 for pairwise alignment, and optionally do
    "prealignment" filters to reduce the number of full alignments that must be
    performed, using EdLib, WFA2 in edit-distance mode, SneakySnake, or a Kmer
    filter. The functions are seq_distmx_edlib() (EdLib, no filter);
    seq_distmx_wfa2() (WFA2 alignment, optional WFA2 edit distance filter);
    seq_distmx_snsn() (WFA2 alignment, SneakySnake filter);
    seq_distmx_kmer() (WFA2 alignment, Kmer distance filter);
    seq_distmx_hybrid() (SneakySnake filter, which routes to EdLib or WFA2
    alignment depending on predicted distance). In a future version these will
    be combined into a single function with options for different methods
  • Introduce seq_clust() function, which calculates pairwise sequence distances
    followed by clustering. Options for sequence distance calculation include
    published libraries edlib and WFA2, as well as fast Hamming distance calculation
    based on code in ProtaxA. Filters are not yet implemented.
  • Add SLINK as a clustering method for seq_clust(), distmx_clust(), and
    distmx_clust_usearch() with cluster_slink(). This classic method is optimal
    when the distances can be guaranteed to be calculated in order.