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IQ-TREE

Purpose: IQ-TREE is a fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. See Explanation for information about this web interface, and see IQ-TREE homepage for details about options.

Input
Paste your alignment here
[Sample Input]
or upload your alignment file

Options
Substitution Model
Sequence type/Model
Nucleotides     Amino acids
Rate heterogeneity
FreeRate model
Gamma model         Alpha (shape parameter) (>0; empty to estimate from data)
  # of rate categories
Create site rates file
State frequency
Estimated by Maximum likelihood
Empirical, computed from alignment input
Empirical, specified in AA model (AA only)
 
Branch Support
Bootstrap Ultrafast         # of replicates         Create bootstrap trees file
standard         # of replicates
Single branch test SH-aLRT branch test         # of replicates
Approximate Bayes test
 
Tree search
Perturbation strength
# of unsuccessful iterations to stop
 
Reconstruct ancestral seqs
Min posterior probability (Threshold to determine the best ancestral state, empty=observed state frequency from input)
User-defined tree
(Enter a tree to see ancestral sequences along it. Otherwise, IQ-TREE computes ancestral sequences of the ML tree)
 
Root tree None     Generalized midpoint optimizationā€ƒ     Simple midpoint     Specify outgroups
Tree type Unrooted     Phylogram     Fan
E-mail Always email results

Reference

Other tree generating tools

last modified: Tue Sep 11 09:48 2018


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

 
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