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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
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.

last modified: Mon Sep 10 09:46 2012


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