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v0.7.0
Pre-release
Pre-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 areseq_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()withcluster_slink(). This classic method is optimal
when the distances can be guaranteed to be calculated in order.