HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


Other HCV databases
The Japanese Hepatitis C Database
The French Hepatitis C Database

Phylogenetics
PHYML
"[...] fast and accurate heuristic for estimating maximum likelihood phylogenies from alignments of homologous sequences. Large DNA and protein sequences data sets can be analysed under a broad range of substitution models. Extensive simulations showed that the topological accuracy of PHYML compares favourably with that of other existing programs, while being much faster."
Splitstree
A web server for the Splitstree program, which allows network as well as tree analysis of phylogenetic (and other) data.
MEGA
A versatile, user-friendly program that does phylogenetic analysis and bootstrapping. PC-Windows.
HyPhy
Another program that does maximum-liklihood trees; it is very flexible and comes with its own programmable interface. This program is probably for the more sophisticated and demanding user. PC-windows, UNIX, Mac.
Tree-Puzzle
"TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. It implements a fast tree search algorithm, quartet puzzling, that allows analysis of large data sets and automatically assigns estimations of support to each internal branch." PC-windows, UNIX, Mac, VMS.
TreeFinder
A very fast ML tree program. "TREEFINDER computes phylogenetic trees from nucleotide sequences using Maximum Likelihood and supports six popular models of sequence evolution up to the general time reversible model with Gamma distributed rates among sites. All model parameters including the rate heterogeneity can be estimated from the data." PC-windows, UNIX, Mac.
Treeview
Treeview displays treefiles; more flexible and easy to use than Drawtree/Drawgram. PC-windows, Mac, Linux/UNIX.
Modeltest
"Modeltest helps a user to choose the model of DNA substitution that best fits his/her data, among 56 possible models." PC-windows, UNIX, Mac.
Phylogenetic Analysis
A comprehensive list of programs for creating phylogenetic trees, maintained by Joe Felsenstein at the University of Washington.

Multiple Sequence Alignment Tools
BioEdit
is a new alignment editor for PC-Windows that allows switching from nucleotide to amino acid view and aligning both simultaneously. It comes with various alignment programs (e.g. Clustal) and tree-building programs (e.g. fastDNAML) built in. Very nifty and up-to-date.
Se-Al
is an alignment editor that is at least as good as BioEdit, unfortunately it is only available for Macs.
Hidden Markov Models
This is a link to the HMMER programs developed by Sean Eddy. We now use HMMs to dynamically generate alignments for our search interface.
CLUSTALX
CLUSTALX is distibuted as executables for DOS/Windows, Mac and UNIX operating systems.
Multiple Sequence Alignment
A collection of alignment programs such as CLUSTALW, for aligning nucleic acid or amino acid sequences. Maintained by the Department of Genetics at the University of Washington, Seattle.
(SAM) - Sequence Alignment and Modeling Programs
Similar to HMMER, this is a package of tools for building and using Hidden Markov Models of multiple sequence alignments. SAM includes programs to convert between the formats for SAM and HMMER.

Other software
Arlequin
Cross-platform Java program for population genetic analysis. Arlequin takes sequence, RFLP, microsatellite, and allele frequency data. It calculates measures of diversity, provides tests for linkage and Hardy_weinberg disequilibrium, and much, much more.
Crann
A program that can test for adaptive evolution, or mutational evidence of selection pressure. Fast, reliable, easy to use, and comes with a very comprehensive and lucid manual.
Datamonkey
Runs a Single Likelihood Ancestor Counting (SLAC) analysis, a heavily modified and efficiently implemented version of the Suzuki-Gojobori method to identify positively and negatively selected sites in a codon alignment.
Simplot
A tool for recombination analysis by Stuart Ray from Johns Hopkins University; it does both similarity plots and bootscan analysis. This tool is by far the most widely used for recombination analysis.
Recombination detection and analysis programs
This page of links is maintained by David Robertson.
The Oxford Evolutionary Biology Group software page
This resource contains many high-quality programs, among them Se-Al (a multiple sequence alignment program for Macs) and many Monte Carlo programs to simulate tree and sequence evolution.
HCV genotyping using BLAST
This ingenious tool allows genotyping without first aligning your sequence to a reference set. The tool is very fast and easy to use, but as with all genotyping and recombination analysis tools, care should be taken in interpreting the results.
SEQUIN
SEQUIN was developed at the NCBI to better handle submissions of large sets of data. SEQUIN can take a multiple sequence alignment as input, and "propagate" features on to all sequences in the alignment, rather than having to annotate features on each sequence individually.
BANKIT
BANKIT is a WWW/HTML-based sequence submission tool. With this tool you can also submit sets of data, but it requires saving the filled out html forms to disk and then re-using the forms after pasting in new data.



Questions or comments? Contact us at hcv-info@lanl.gov