Change log

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Major changes to BioKIT are summarized here.

0.1.0: Functions that remove adapters from FASTQ files (trim_se_adapters_fastq and trim_pe_adapters_fastq) are now part of BioKIT. Note, these identify exact matches of adapters.

Parsimony informative sites, constant sites, and variable sites functions now have a verbose option that allows users to examine the characterization of each site in an alignment.

The name gw-RSCU has been shortened to gRSCU.

0.0.9: Functions that look at codons (e.g., RSCU and gw-RSCU) now can account for ambiguous codons. For example, codons that have ambiguous characters like the codon “CNN.” These codons are skipped during analysis of RSCU and gw-RSCU.

1.0.1: Added “X” as a gap character during alignment recoding

1.1.0: Added Dayhoff-9, -12, -15, and -18 recoding schemes

1.1.3: Fixed bug in RSCU calculations