Analysis and Quality Control
Entropy quantifies positional variation in an alignment using Shannon Entropy 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 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 characterizes features within a peptide excised from a protein alignment, summarizing and reporting the following peptide characteristics: length, number of N-linked glycosylation sites. It is particularly useful for characterizing hypervariable regions in Env. VESPA (Viral Epidemiology Signature Pattern Analysis) detects residues with different frequencies in two sequence sets Alignment and sequence manipulation
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 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
ELF (Epitope Location Finder) identifies known and potential epitopes within peptides 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 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 CATNAP (Compile, Analyze, Tally NAb Panels) provides meta-analysis of published neutralization panel data PeptGen generates overlapping peptides from a protein sequence Database search interfaces
Advanced Search creates a custom search interface Antibodies search for HIV antibodies by protein, immunogen, AB type, isotype, author, keywords CTL/CD8+ Search searches for CD8+ epitopes by protein, immunogen, HLA, author, keywords Geography shows the geographic distribution of sequences in the database Reference Sequence Coordinate Search retrieves HXB2 and Mac239 features and coordinates Intra-patient Search retrieves intra-patient sequence sets Neutralizing Antibody Contexts and Features retrieves information about neutralizing antibodies Sequence Search searches for sequences based on numerous criteria T-Helper/CD4+ Search search for CD4+ epitopes by protein, immunogen, HLA, author, keywords Vaccine Trials Database finds past vaccine trials and their results Additional Resources
External tools tools and programs on other websites |