Adds the terminal-ambiguity trimming step to the Zika page GenBank processing trims terminal ambiguous nucleotides and drops sequences outside a length range before annotation, so results from an untrimmed file can differ from what GenBank reports. The other per-virus pages document this step; the Zika page did not. Uses --minlen 50 --maxlen 12000. The RefSeq NC_035889 is 10,808nt, so 12,000 leaves room for the longer real sequences while still catching anything unexpectedly long. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CRGu3BmwzMzTWDdjpLSxVo
Adds a Zika virus annotation page Covers installing VADR 1.7.1 or later, downloading the zika models, the recommended v-annotate.pl options and what each does, the clade classification output, and structure drawing with --draw_r2dt. Documents that the INDEFINITE_CLASSIFICATION_NN alert fires on nearly every Zika sequence, since Zika's clades are separated by far less divergence than the default threshold anticipates, and that the alert is never fatal. No specific --nn_indefclass value is recommended: the gap distribution is narrow enough that the flag rate is very sensitive to the threshold chosen, and there is no dataset of genuine Zika clade misclassifications against which a tighter one could be shown not to miss real cases. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CRGu3BmwzMzTWDdjpLSxVo