Corrected usage in cdhit-utility.c++#51
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The usage presented in the tools in the CD-HIT suite that take nucleotide sequences as input is incorrect. For example, when one calls cd-hit-est (v4.7), there are references to amino acids: <pre> -c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical <b>amino acids</b> in alignment divided by the full length of the shorter sequence </pre> There are several small inconsistencies throughout the usage; I have fixed them throughout the cdhit-utility.c+++ file.
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The usage presented in the tools in the CD-HIT suite that take nucleotide sequences as input is incorrect. For example, when one calls
cd-hit-est(v4.7), there are references to amino acids, e.g.:There are several small inconsistencies throughout the usage; I have made the appropriate fixes to the
cdhit-utility.c++file so that when one calls a nucleotide sequence tool, one sees 'nucleotide' or 'nt,' and when one calls a protein sequence tool, one sees 'amino acid' or 'aa.'These changes are all cosmetic, but as a user of the tool, I have been confused in the past about which tool I was using, or wanted to use, after reading the usage.