Download function identifies problem GIs and skips them if they continue causing problems.
Adds a small hack that prevents location_from_string function from crashing under certain rare conditions.
Minor performance adjustments for phylo workflow.
Lets user choose if write_log function should print to file, screen or both.
Minor UI improvements.
Updates improve_alignment_using_reference_records function, so it reduces the required identity with each iteration to produce the results faster.
Adds merge_subspecies and merge_varieties functionality.
Minor adjustments in KRSequenceDatabase. Also adds full lineage information and common name support.
Messages are printed without a dash between timestamp.
Adds common name support.
Adds functions that deal with common names and lineages.
Fixes a bug where identity for an alignment would be miscalculated if the sequences in a pairwise alignment did not overlap. Enhances cluster function, it is now possible to define a list of seed sequences. Adds dereplicate function.
Integrates new functionality: common name, lineage, better filtering with dereplicated seeds.
Updates default config file and adds new search strategies.
Silences all logging for phylo workflow.
Fixes a bug where consensus function did not treat 'N' as an unknown nucleotide.
Updated template config file and search strategies. Adds support for outgroup separation.
Adds reset database, autopilot, and outgroup separation functionality. Enables logging output.
Updated search strategies and config file.
Adds new and faster identity function. Adds pairwise_coverage function. Comments old identity and pairwise_identity functions.