Version 0.0.5

This update comprises a major enhancement to scripts that carry out a procedure converting ARIBA outputs into an allelic PAM. Alleles gathered by this procedure are now named after their best matches in the reference database rather than after cluster names of reference alleles, making it easier to interpret results.

PAMmaker v0.0.4

This release enables conversion of ARIBA outputs into an allelic PAM.

v0.0.3

Completed documentation and adjusted directory structure. Minor changes applied to a few scripts.

Correcting allele names for the same consensus sequences

This is a profound update of algorithms, which corrects allele names when the same consensus sequence is aligned to multiple reference alleles in different strains. This problem caused split of allele calls when they actually reveal the same allele. This update also enables PAMmaker to take as input the clustering outcome when consensus sequences are clustered at a nucleotide identity of <100%.

v0.0.1: first public release

Add Count_score for maxMAFstats.R