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- seq.filter - Remove select columns from an alignment by removing any column that has a specific character in it, a minimum base frequency, or a user-supplied filter
- dist.seqs - Generate pairwise distance matrix in column format
- tree.shared - Generate a newick-formatted tree file comparing the membership or structure of multiple communities
- Shared Chao1 richness estimator for N≥2; incorporated into calculating 3- and 4-way Venn diagrams
- Got rid of weird output to screen when running collect.single() or using the npshannon calculator
- Fixed bug that would not permit freq=1
- Fixed file error with rarefaction.single() and rarefaction.shared()