What should I use as a reference in hivmmer
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2.2 years ago

I am unable to figure out what my reference should be to be used for the hivmmer tool (version 0.1.2) for HIV genotyping. I tried building a profile Hidden Markov Model file by using hmmer (version 3.2.1) and I am getting the following error when trying to build a profile hidden Markov Model file using the hmmbuild command from a multiple sequence alignment amino acid sequences fasta file.

Alignment input parse error: while reading aligned FASTA file HIV1_ALL_2018_pol_PRO.fasta at or near line 39

I noticed that hivmmer also has prepackaged profile hidden markov models but how can I access them? I would really appreciate if if someone can help me to figure this out.

HIV genotyping hivmmer hmmer HMM • 498 views

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