HIV Database Tools
Tools specific for HIV/SIV
General use tools with some HIV/SIV-specific features
General use tools
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
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
Align Multi-tool
manipulates sequence alignments, including sorting, pruning, and renaming
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
ElimDupes
compares the sequences within an alignment and eliminates any duplicates
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
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
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
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
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
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)
Motif Scan
finds HLA anchor motifs in protein sequences for specified HLA serotypes, genotypes or supertypes
PeptGen
generates overlapping peptides from a protein sequence
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
last modified: Thu Feb 8 12:38 2024