[TOC] Layout Generators ----------------- - Sequencing [layout designer](/django/tools/sequencing_layout/) - Sequencing plate layout [archive](/django/tools/sequencing_layout/output/) (You need an account to access this page) <br><br> - 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 ---------------------- - 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 ------------------------------ - 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 ------------------------------- - 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/) <br><br> TCR interpretation and analysis ------------------------------- - 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/