├── .gitignore ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── NEWS ├── README.md ├── hivmmer ├── VERSION ├── __init__.py ├── codons.py ├── consensus.py ├── drms.csv ├── drms.py ├── env.hmm.h3f ├── env.hmm.h3i ├── env.hmm.h3m ├── env.hmm.h3p ├── env.hxb2.tsv ├── filter.py ├── gag.hmm.h3f ├── gag.hmm.h3i ├── gag.hmm.h3m ├── gag.hmm.h3p ├── gag.hxb2.tsv ├── nef.hmm.h3f ├── nef.hmm.h3i ├── nef.hmm.h3m ├── nef.hmm.h3p ├── nef.hxb2.tsv ├── pol.hmm.h3f ├── pol.hmm.h3i ├── pol.hmm.h3m ├── pol.hmm.h3p ├── pol.hxb2.tsv ├── report.py ├── table.py ├── tat.hmm.h3f ├── tat.hmm.h3i ├── tat.hmm.h3m ├── tat.hmm.h3p ├── tat.hxb2.tsv ├── translate.py ├── vif.hmm.h3f ├── vif.hmm.h3i ├── vif.hmm.h3m ├── vif.hmm.h3p ├── vif.hxb2.tsv ├── vpr.hmm.h3f ├── vpr.hmm.h3i ├── vpr.hmm.h3m ├── vpr.hmm.h3p ├── vpr.hxb2.tsv ├── vpu.hmm.h3f ├── vpu.hmm.h3i ├── vpu.hmm.h3m ├── vpu.hmm.h3p └── vpu.hxb2.tsv ├── scripts └── hivmmer ├── setup.py ├── test ├── 5VM_1.fastq ├── 5VM_2.fastq ├── drms.csv └── test.sh └── validation ├── README.md ├── SConstruct ├── data ├── HIV1_FLT_2017_env_PRO.fasta ├── HIV1_FLT_2017_gag_PRO.fasta ├── HIV1_FLT_2017_nef_PRO.fasta ├── HIV1_FLT_2017_pol_PRO.fasta ├── HIV1_FLT_2017_tat_PRO.fasta ├── HIV1_FLT_2017_vif_PRO.fasta ├── HIV1_FLT_2017_vpr_PRO.fasta ├── HIV1_FLT_2017_vpu_PRO.fasta └── wgs-hxb2-coordinates.csv ├── evalue-5VM.png ├── evalue-reference.png ├── evalue.png └── lib ├── filter.py ├── hmmsearch-csv.sh ├── hxb2-index.py ├── merge-csv.py ├── plot-evalue-reference.R ├── plot-evalue.R ├── randomize-data.py ├── reference-data.py ├── reference-len.py └── trim-reference.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kantorlab/hivmmer/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/kantorlab/hivmmer/HEAD/Dockerfile 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