HIV Databases HIV Databases home HIV Databases home
HIV sequence database

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.

Paste your alignment here
[Sample Input]
or upload your alignment file
Is it in relaxed phylip?
(seq name length>10)
no  relaxed sequential phylip  relaxed interleaved phylip 

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
User tree (in Newick format)
Tree improvement
Branch Support Approximate Likelihood Ratio Test (aLRT)  
Bootstrap    # of replicates
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.

last modified: Wed Apr 1 09:45 2015

Questions or comments? Contact us at

Operated by Los Alamos National Security, LLC, for the U.S. Department of Energy's National Nuclear Security Administration
Copyright © 2005-2012 LANS LLC All rights reserved | Disclaimer/Privacy

Dept of Health & Human Services Los Alamos National Institutes of Health