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HIV Sequence Database



HIV Database Tools

Tools specific for HIV/SIV
General use tools with some HIV/SIV-specific features
General use tools
Analysis and Quality Control
Entropy quantifies positional variation in an alignment using Shannon Entropy
GenSig identifies genetic signatures. It can work on any phenotype file given in conjunction with a codon-aligned nucleotidealignment of a protein coding region
Glycan Shield Mapping shows a mapping of absent hole-causing potential N-linked glycosylation sites on predicted glycan shields for a HIV/SIV Env sequence
HIV BLAST finds sequences similar to yours in the HIV database
Hypermut detects hypermutation
jpHMM at GOBICS detects subtype recombination in HIV-1; hosted at GOBICS as a collaboration between the Department of Bioinformatics, University of Göttingen and the Los Alamos HIV Sequence Database
N-Glycosite finds potential N-linked glycosylation sites
PCOORD multidimensional analysis of sequence variation
Quality Control runs several tools for quick troubleshooting of HIV-1 sequences; optional step prepares sequence submission for GenBank
RAPR (Recombinant Analysis PRogram) uses the Wald-Wolfowitz Runs Test to check for recombination in every triplet in the alignment.
RIP (Recombinant Identification Program) detects HIV-1 subtypes and recombination
SNAP calculates synonymous/non-synonymous substitution rates
SUDI Subtyping plots the distance of your sequence to established subtypes
Variable Region Characteristics summarizes features of peptides from a protein alignment, reporting peptide characteristics such as length and N-linked glycosylation sites; particularly useful for characterizing variable regions of Env
VESPA (Viral Epidemiology Signature Pattern Analysis) detects residues with different frequencies in two sequence sets
Alignment and sequence manipulation
Align Multi-tool manipulates sequence alignments, including sorting, pruning, and renaming
Alignment Slicer cuts vertical slices from sequence alignments
Analyze Align shows weblogos, calculates frequency by position, and finds variants in an alignment
Codon Alignment takes a nucleotide alignment and returns a codon alignment and translation
Consensus Maker computes a customizable consensus
ElimDupes compares the sequences within an alignment and eliminates any duplicates
Gap Strip/Squeeze removes columns with more than a given % of gaps
Gene Cutter clips genes from a nucleotide alignment, codon-aligns, and translates
HIValign uses our HMM alignment models to align your sequences
PepMap can be used to map epitopes, functional domains, or any protein region of interest
Pixel generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue
QuickAlign (formerly Epilign and Primalign) aligns short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments, or to a user alignment
Sequence Locator finds the standard numbering of your HIV or SIV nucleotide or protein sequence
SynchAlign aligns overlapping alignments to one another
Translate nucleotide sequences to 1-letter amino acids
Format and display
Format Converter converts between alignment formats
GenBank Entry Generation produces GenBank Sequin files for HIV-1, HIV-2, and SIV sequences, plus associated metadata
Genome Browser uses jBrowse to display diverse data about the HIV-1 genome and proteome
Highlighter highlights mismatches, matches, transitions and transversion mutations and silent and non-silent mutations in an alignment of nucleotide sequences
Protein Feature Accent provides an interactive 3-D graphic of HIV proteins; can map a sequence feature (a short functional domain, epitope, or amino acid) and see it spatially
Recombinant HIV-1 Drawing Tool creates a graphical representation of your HIV-1 intersubtype recombinant
SeqPublish makes publication-ready alignments
Phylogenetics
AnnotateTree creates a colored and weighted phylogenetic tree
Branchlength calculates branch lengths between internal and end nodes; now included in the TreeRate tool
FindModel finds which evolutionary model best fits your sequences
IQ-TREE is a fast and effective stochastic algorithm for finding Maximum Likelihood trees, including site-specific rates of evolution at each alignment position
PhyloPlace reports phylogenetic relatedness of an HIV-1 sequence with reference sequences
PhyML generates much better trees than our simple TreeMaker tool
Poisson-Fitter estimates time since MRCA and star-phylogeny. For use with acute (low diversity) samples
Rainbow Tree Color code phylogenetic tree branches according to labels in the sequence names
TreeMaker generates a Neighbor Joining phylogenetic tree
TreeRate finds the phylogenetic root of a tree and calculates branch lengths and evolutionary rate
Immunology
CAByN (Choose Antibodies By Neutralization) returns all antibodies meeting selected criteria for HIV-1 neutralizing activity
CATNAP (Compile, Analyze, Tally NAb Panels) provides published neutralization data and tools for analysis
CombiNAber predicts and analyzes combination antibody neutralization scores using IC50 and/or IC80 for individual antibodies
ELF (Epitope Location Finder) identifies known and potential epitopes within peptides
Epigraph Tool Suite uses input of diverse sequences to generate Epigraph sequences for use in vaccine or reagent design
Epilign (QuickAlign) aligns a protein sequence (e.g., epitope) to the appropriate protein alignment
Heatmap displays a table of numbers by using colors to represent the numerical values
Hepitope identifies potential epitopes based on HLA frequencies
Neutralization Index computes a tier-like score for sera (using ID50 titers) or antibodies (using IC50 titers)
Mosaic Vaccine Tool Suite designs and assesses polyvalent protein sequences for T-cell vaccines
Motif Scan finds HLA anchor motifs in protein sequences for specified HLA serotypes, genotypes or supertypes
PeptGen generates overlapping peptides from a protein sequence
Database search interfaces
Antibodies search for HIV antibodies
Epitope Search: CTL/CD8+ search for CD8+ epitopes by protein, immunogen, HLA, author, keywords
Epitope Search: T-Helper/CD4+ search for CD4+ epitopes by protein, immunogen, HLA, author, keywords
Geography (old) shows the geographic distribution of HIV sequences in the database
Geography (new) shows the geographic distribution of HIV sequences in the database, with the option to view by time range
Reference Sequence Coordinate Search retrieves HXB2 and Mac239 features and coordinates
Neutralizing Antibody Contacts and Features retrieves neutralizing antibody contact sites and other HIV-1 Env features
Sequence Search searches for sequences based on numerous criteria
Sequence Advanced Search creates a custom search interface based on database tables
Sequence Intra-patient Search retrieves intra-patient sequence sets
Vaccine Trials Database (no longer maintained)
Additional Resources
External tools tools and programs on other websites



last modified: Thu Feb 8 12:38 2024


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