v1.0.8

• fixes inconsistencies between loading directly via the import_fasta_sparse_nt function or loading an MSA initially using ape. The latter could lead to the program crashing when gaps or Ns were included in the alignment.

v1.0.7

• Fixes a bug in very small alignments loaded from FASTA files. The initial sequence was not counted in the definition of the consensus variant. This led to problems when a variant was only present twice and one of these examples was in the first sequence.
• Adds a better error message when there is less than two variants from which to perform the clustering.

v1.0.6

Fixes bugs in the import_fasta_sparse_nt.R script.

• Resolves an issue that caused a stack overflow on very large alignments when loading directly from file
• Resolves an issue that caused an error when an alignment generated using ape was loaded directly and included a column that was mostly gaps.

v1.0.4

• update dependencies
• fix spelling error

v1.0.3

• added command line script
• updated documentation

v1.0.2

Release with latest minor changes for conda

zenodo release

v1.0.1

pre-release cleaning updates

initial release

Release for publication on biorxiv