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.


PhyML Interface

Purpose: To provide an interface to PhyML, a fast and flexible program that generates good maximum likelihood trees. See PhyML 3.0 for information about PhyML; see PhyML Explanation for information about this web interface.

Input
 ** Submit long-name-sequences (>10 chars) as any format other than phylip (about phylip format)
Paste your alignment here
[Sample Input]
or upload your alignment file

Options
Substitution Model
Sequence type/Model Nucleotides      Amino acids 
Equilibrium frequencies Empirical    Estimated using Maximum likelihood(nt) or Model(aa)
Transition/Transversion ratio
(nt only)
(positive number; leave empty to estimate from data)
Proportion of invariable sites (0.0-1.0 ; leave empty to estimate from data)
Gamma shape parameter (positive number; leave empty to estimate from data)
# of substitution rate categories (positive integer)
 
Tree Searching
Starting tree(s) optimization
Starting tree(s) BioNJ
Parsimony
User tree (in Newick format)
Tree improvement
 
Branch Support Approximate Likelihood Ratio Test (aLRT)  
Bootstrap    # of replicates
None
 
Outgroup Specify outgroup
E-mail Always email results

If you use this tool, please cite this paper:
Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology, 59(3):307-21, 2010.


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