[TOC]

Layout Generators
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- Sequencing [layout designer](/django/tools/sequencing_layout/)
- Sequencing plate layout [archive](/django/tools/sequencing_layout/output/) (You need an account to access this page)
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- Guava [layout designer](/django/tools/guava_layout/)
- Guava plate layout [archive](/django/tools/guava_layout/output/) (You need an account to access this page)

QC and data processing
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- Fasta Converter in house [fasta-csv conversion tool](/django/tools/fasta_converter/)
- Text to columns [Text to Columns tool](/django/tools/text_to_columns/)
- False discovery rate [q-value calculator](/django/tools/qvalue/)

HIV sequence/function analyses
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- HXB2 Genome [genome map](/django/tools/HIV_genome/)
- DNA translator [DNA translation tool](/django/tools/translate_DNA/)
- Quality Checker [Quality Check Tool](/django/tools/quality_check/)
- Unique Sequence Finder [USF](/django/tools/unique_sequence/)
- Variable Function Analysis [in house variable-function analyzer](/django/tools/variable_function/)
- Codon by codon in house [analysis tool](/django/tools/codon_by_codon/)
- [Phylogenetic Dating](/django/tools/phylodating/)


HLA interpretation and analyses
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- HLA class I sequence-based typing [interpretation tool](/django/tools/hla_class/)
- PHAGE-I-expanded - Proportion of HLA Associated Genomic Escape (individual). [PHAGE-I-expanded](/django/tools/phage_i_expanded/)
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TCR interpretation and analysis
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- TCR Distance [convert cellranger output for TCR Visualizer](/django/tools/tcr_distance/)
- TCR Visualizer [network diagram visualization](/django/tools/tcr_visualizer/)


Other useful resources
----------------------
- [Primer tables](/django/wiki/misc/primer-list/) for sequencing or PCR
- [Papers](/django/wiki/misc/papers/) about HIV virology, epidemiology, immunology
- Stanford Drug Resistance Database: https://hivdb.stanford.edu/
- LANL HIV Sequence database: https://www.hiv.lanl.gov/content/sequence/HIV/mainpage.html/
- LANL HIV Immunology Database: https://www.hiv.lanl.gov/content/immunology/index.html/