List of Acronyms and Abbreviations

AA: Amino Acid
AIDS: Acquired Immunodeficience Syndrome
ART: Antiretroviral therapy
BLAST: Basic Local Alignment Search Tool
BLOSUM: Block Substitution
CCS: Circular Consensus Sequencing
CRF: Circulating Recombinant Form
DNA: Desoxy Ribonucleic Acid
dNTP: deoxyNucleotide Triphosphate
DRM: Drug Resistance Mutation
EI: Entry Inhibitor
FI: Fusion Inhibitor
HIV: Human Immunodeficiency Virus
HMM: Hidden Markov Model
HPC: Homopolymer Compression
IN: Integrase
INSTI: Integrase Strand Transfer Inhibitor
LR: Logisitic Regression
mapq: mapping quality
ML: Machine Learning
MSA: Multiple Sequence Alignment
MSR: Mapping-friendly sequence reduction
NNIBP: Non-Nucleoside Reverse Transcriptase Inhibitor Binding Pocket
NNRTI: Non-Nucleoside Reverse Transcriptase Inhibitor
NRTI: Nucleoside Reverse Transcriptase Inhibitor
NTP: Nucleotide Triphosphate
NW: Needleman Wunsch algorithm
ONT: Oxford Nanopore Technologies
PacBio: Pacific Biosciences
PAM: Point Accepted Mutation
PE: Pharmacokinetic Enhancer
PI: Protease Inhibitor
PR: Protease
RAM: Resistance Associated Mutation
RC: reverse complement
RF: Random Forest
RNA: Ribonucleic Acid
RR: Risk Ratio
RT: Reverse Transcriptase
RTI: Reverse Transcriptase Inhibitor
SSR: Streaming sequence reduction
SW: Smith Waterman algorithm