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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
or upload your alignment file
Is it in relaxed phylip?
(seq name length>10)
no  relaxed sequential phylip  relaxed interleaved phylip 

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) BioNJ
Parsimony
User tree (in Newick format)
Tree optimization
Tree improvement
 
Branch Support Approximate Likelihood Ratio Test (aLRT)  
Bootstrap    # of replicates
None
 
Outgroup Specify outgroup
E-mail Always email results

Reference

Other tree generating tools

Maximum likelihood tree generating tools

last modified: Tue Sep 19 13:47 2017


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

 
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