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HIV sequence database


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.

Paste your alignment here
or upload your alignment file

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 optimization icon     Simple midpoint icon    Specify outgroups
Tree type Unrooted     Phylogram     Fan
E-mail Always email results


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last modified: Wed May 29 08:38 2019

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