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Sequence Searches
Search Interface: Filoviruses retrieves filovirus virus sequences Search Interface: HFV retrieves sequences for all hemorrhagic fever viruses Advanced Search creates a customized search interface Alignments
Filovirus Premade Alignments are manually optimized alignments for viruses that belong to Ebolavirus, Marburgvirus, and Cuevavirus genera HFV Premade Alignments are manually optimized genus reference alignments for all hemorrhagic fever viruses Immunology Resources
Ebolavirus and Marburgvirus Immunology Resources provides information about filovirus T-cell epitopes and antibodies Epitope Maps show the location of ebolavirus and marburgvirus epitopes, relative to reference sequences Geography Resources
Global Outbreak Maps show global distribution of Ebola & Marburg diseases Geography Search: Filoviruses retrieves filovirus sequences based on geographical distribution Geography Search: HFV retrieves HFV sequences based on geographical distribution Genome Coordinate Resources
Genome Coordinate Resources provides genome coordinates and spreadsheet data for features of filovirus sequences Filovirus Coordinates and Naming provides information about the ebolavirus reference sequence and the sequence naming systems used for all filoviruses on this website Sequence Manipulation Tools
AnalyzeAlign shows weblogos, calculates frequency by position, and finds variants in an alignment CodonAlign takes nucleotide alignment and returns codon alignment and translates to protein sequences Consensus computes a customizable consensus Gapstreeze removes columns with more than a given % of gaps HFValign aligns your sequence(s) using either the multiple alignment program MAFFT, or using the appropriate hidden Markov model. PeptGen generates overlapping peptides from a protein sequence Pixel generates a PNG image of an alignment using 1 or more colored pixel(s) for each residue QuickAlign aligns short nucleotide or protein sequences (e.g., primers, epitopes) to our prebuilt genome or protein alignments, or to a user alignment Sequence Locator aligns your nucleotide or protein sequence to a reference genome and shows feature and coordinate information Translate nucleotide sequences to 1-letter amino acids |
Format and Display Tools
Ebola Genome Browser provides interactive views of the ebolavirus genome and proteome Genome Mapper creates a genomic feature map for any HFV organism Format Converter converts between 18 standard sequence formats SeqPublish is to make publication-ready alignments Analysis Tools
HFV BLAST finds sequences similar to yours in the HFV database. Highlighter shows matches, mismatches and mutations in an aligned set of nucleotide sequences. N-Glycosite find potential N-linked glycosylation sites in a protein alignment PCOORD multidimensional analysis of sequence variation SNAP calculates synonymous/non-synonymous substitution rates VESPA detects signatures: residues with different frequencies in two sequence sets Phylogenetics Tools
FindModel finds which evolutionary model best fits your sequences PhyloPlace reports phylogenetic relatedness of query sequence with reference sequences in known clades. PhyML interface creates and displays a Maximum-Likelihood tree using the PhyML code; many evolutionary models can be specified Rainbow Tree color codes phylogenetic tree branches according to labels in the sequence names TreeMaker generates a quick-and-dirty phylogenetic tree TreeRate calculates branch lengths between internal and end nodes based on a Newick treefile External Tools and Resources
External Resources links to additional resources on other websites |