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iqtree: Construct a phylogenetic tree with IQ-TREE.

Citations

[phylogeny:iqtree:KMW+17]Subha Kalyaanamoorthy, Bui Quang Minh, Thomas K F Wong, Arndt von Haeseler, and Lars S Jermiin. Modelfinder: fast model selection for accurate phylogenetic estimates. Nature Methods, 14(6):587–589, 2017. URL: http://dx.doi.org/10.1038/nmeth.4285, doi:10.1038/nmeth.4285.
[phylogeny:iqtree:NSvHM15]Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler, and Bui Quang Minh. Iq-tree: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 32(1):268–274, 2015. URL: http://dx.doi.org/10.1093/molbev/msu300, doi:10.1093/molbev/msu300.

Docstring:

Usage: qiime phylogeny iqtree [OPTIONS]

  Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
  automatic model selection.

Options:
  --i-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  Aligned sequences to be used for
                                  phylogenetic reconstruction.  [required]
  --p-seed INTEGER                Random number seed. If not set, program
                                  defaults will be used. See IQ-TREE manual
                                  for details.  [optional]
  --p-n-cores INTEGER RANGE       The number of cores to use for parallel
                                  processing. Use '0' to let IQ-TREE
                                  automatically determine the optimal number
                                  of cores to use.  [default: 1]
  --p-n-runs INTEGER RANGE        Number of indepedent runs. Multiple
                                  independent runs (e.g. 10) can outperform a
                                  single run in terms of likelihood
                                  maximisation.  [default: 1]
  --p-substitution-model [TVMe+R4|K80+R6|TNe+R6|TPM3+I|F81+R3|HKY+G|TPM3|TIMe|TIM+R4|F81+R9|GTR|TVMe+R5|K80|TPM3u+R7|TVM+R6|K80+R2|TNe+R10|TIM2+R4|HKY+I+G|TPM2u+G|TNe+R8|TNe+I|TIM2e+R6|K80+R4|TIM3e+I+G|TNe+R5|JC+R6|JC|K81|HKY+R10|GTR+R6|TVMe+R6|F81+I+G|TIMe+I+G|SYM+R6|F81+R5|TPM2+R3|TVM+G|K80+R5|TIM2+R10|TIM2e+R4|SYM+I|TIM+R3|TIM3e+R2|K81+R5|TVM+R2|TPM2u+R8|TPM2+R10|JC+R4|K81u+I|GTR+I+G|TPM3u+R4|K81u+I+G|TPM2u+I+G|TPM2u+R7|TPM2+R9|K81+G|K81u+G|TN+R2|TIM+R6|K81+I+G|TPM2+I+G|TPM3u+I+G|TIMe+R3|TIM2e+R7|HKY+R3|TPM3+R7|TIM2e+I+G|TIM+G|TIM3e+R7|TIM2+R2|TVMe+G|JC+I+G|F81+R8|K80+G|JC+R10|TPM3+R5|TPM3u+R9|TIMe+R8|TIM2e+R8|TVMe|TIM3+R4|TVM|TIM3+G|TN+R7|TPM2+R5|TNe|TIM+R9|TPM3+R8|TIM3+R8|TVMe+R10|K81+R6|GTR+R9|TIM2e+I|TVM+R8|SYM+I+G|TIM3e+R5|TPM2u+R4|K81+R7|TIM+I|TN+R5|TIM3e+R9|TIM2+R8|GTR+R2|TNe+R9|TPM3+R4|K80+I+G|TPM2+R8|TIM2+G|TN+I|K81u|TIMe+R7|TVM+R5|HKY|TIM3+R2|GTR+R5|MFP|TIM+R7|TN+R3|TPM3u+G|JC+R7|TNe+R4|TNe+G|TIM3|HKY+R4|K80+R10|SYM|TVM+R3|TIM2e+R3|TVMe+I|HKY+I|JC+G|TIM2|TIM2e+R2|TPM2u+R2|K81+R9|K81u+R8|K81+I|TPM2+R7|K81+R2|TPM2u+I|TIM3+R6|F81+R2|TN+G|TNe+I+G|K81u+R9|TIMe+R9|TIM+R5|TIM2+R3|SYM+G|TIM3+I+G|JC+R2|TIM3+R5|HKY+R9|TPM2+R6|TVMe+R7|TN+R8|K81+R4|JC+R5|TIM2+I+G|K80+R7|HKY+R6|K81u+R7|TIMe+R2|TPM3+R9|JC+R8|K81u+R4|SYM+R5|GTR+R4|F81+G|HKY+R2|K81u+R10|SYM+R2|TPM2+G|TIM2+R9|K81u+R5|TNe+R2|TIM3e+R3|SYM+R3|TN+I+G|TPM3+G|TIM2+I|TPM3u+R2|TIM2+R5|SYM+R8|TIM+R10|TIM2e+R9|TIMe+G|TVM+R7|TVM+I+G|TIM3e+R4|GTR+R7|TPM2u+R9|TNe+R7|TIMe+R4|TPM2u+R6|TVMe+R3|TVM+R10|TN|SYM+R9|TVM+R4|SYM+R10|K81+R10|TN+R9|TIM3e+R6|F81+R10|TPM2u+R5|F81+R7|K81u+R2|TIM3e+R10|TVM+I|TPM3u+I|K80+R3|TPM2+R4|JC+R9|F81+R6|F81|K81+R8|TIMe+R6|TVMe+R8|TIM3+I|GTR+R3|TIM+R2|K80+R8|HKY+R5|TIMe+I|TIM2e+R5|TPM2u+R10|TIMe+R5|K81+R3|TPM3u+R10|TPM3+R10|HKY+R7|TNe+R3|TPM2u+R3|TIM3+R9|TPM2+I|TIM2e|GTR+R8|TIM|TPM3+R6|TIM2e+G|TIM2+R6|TN+R6|TIM2+R7|F81+I|TPM3+I+G|TPM2|TPM3u+R3|TIM3e+G|TIM3e+R8|SYM+R7|TPM2+R2|TIM3+R7|TPM3u|GTR+G|F81+R4|GTR+R10|TPM3u+R5|TPM3u+R8|TIM+R8|TIM+I+G|HKY+R8|TN+R10|TVMe+R2|TN+R4|K80+R9|TVM+R9|TIM3+R10|JC+R3|TVMe+I+G|TIM3e|TPM3u+R6|TIMe+R10|GTR+I|TIM2e+R10|TEST|JC+I|K80+I|K81u+R6|TPM3+R2|K81u+R3|TPM3+R3|TIM3e+I|TIM3+R3|TVMe+R9|SYM+R4|TPM2u]
                                  Model of Nucleotide Substitution. If not
                                  provided, IQ-TREE will determine the best
                                  fit substitution model automatically.
                                  [default: MFP]
  --p-n-init-pars-trees INTEGER RANGE
                                  Number of initial parsimony trees. If not
                                  set, program defaults will be used. See IQ-
                                  TREE manual for details.  [optional]
  --p-n-top-init-trees INTEGER RANGE
                                  Number of top initial trees. If not set,
                                  program defaults will be used. See IQ-TREE
                                  manual for details.  [optional]
  --p-n-best-retain-trees INTEGER RANGE
                                  Number of best trees retained during search.
                                  If not set, program defaults will be used.
                                  See IQ-TREE manual for details.  [optional]
  --p-n-iter INTEGER RANGE        Fix number of iterations to stop. If not
                                  set, program defaults will be used. See IQ-
                                  TREE manual for details.  [optional]
  --p-stop-iter INTEGER RANGE     Number of unsuccessful iterations to stop.
                                  If not set, program defaults will be used.
                                  See IQ-TREE manual for details.  [optional]
  --p-perturb-nni-strength FLOAT  Perturbation strength for randomized NNI. If
                                  not set, program defaults will be used. See
                                  IQ-TREE manual for details.  [optional]
  --p-spr-radius INTEGER RANGE    Radius for parsimony SPR search. If not set,
                                  program defaults will be used. See IQ-TREE
                                  manual for details.  [optional]
  --p-allnni / --p-no-allnni      Perform more thorough NNI search.  [default:
                                  False]
  --p-fast / --p-no-fast          Fast search to resemble FastTree.  [default:
                                  False]
  --p-alrt INTEGER RANGE          Single branch test method. Number of
                                  bootstrap replicates to perform an SH-like
                                  approximate likelihood ratio test (SH-aLRT).
                                  Minimum of 1000 replicates is recomended.
                                  Set to '0' for parametric aLRT test. Can be
                                  used with other 'single branch test
                                  methods'. Values reported in the order of:
                                  alrt, lbp, abayes.  [optional]
  --p-abayes / --p-no-abayes      Single branch test method. Approximate Bayes
                                  test. Can be used with other 'single branch
                                  test methods'. Values reported in the order
                                  of: alrt, lbp, abayes.  [default: False]
  --p-lbp INTEGER RANGE           Single branch test method. Number of
                                  bootstrap replicates to perform a fast local
                                  bootstrap probability method. Minimum of
                                  1000 replicates is recomended. Can be used
                                  with other 'single branch test methods'.
                                  Values reported in the order of: alrt, lbp,
                                  abayes.  [optional]
  --p-safe / --p-no-safe          Safe likelihood kernel to avoid numerical
                                  underflow.  [default: False]
  --o-tree ARTIFACT PATH Phylogeny[Unrooted]
                                  The resulting phylogenetic tree.  [required
                                  if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.phylogeny.methods import iqtree

Docstring:

Construct a phylogenetic tree with IQ-TREE.

Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
automatic model selection.

Parameters
----------
alignment : FeatureData[AlignedSequence]
    Aligned sequences to be used for phylogenetic reconstruction.
seed : Int, optional
    Random number seed. If not set, program defaults will be used. See IQ-
    TREE manual for details.
n_cores : Int % Range(0, None), optional
    The number of cores to use for parallel processing. Use '0' to let IQ-
    TREE automatically determine the optimal number of cores to use.
n_runs : Int % Range(1, None), optional
    Number of indepedent runs. Multiple  independent runs (e.g. 10) can
    outperform a single run in terms of likelihood maximisation.
substitution_model : Str % Choices({'F81', 'F81+G', 'F81+I', 'F81+I+G', 'F81+R10', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'GTR', 'GTR+G', 'GTR+I', 'GTR+I+G', 'GTR+R10', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'HKY', 'HKY+G', 'HKY+I', 'HKY+I+G', 'HKY+R10', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'JC', 'JC+G', 'JC+I', 'JC+I+G', 'JC+R10', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'K80', 'K80+G', 'K80+I', 'K80+I+G', 'K80+R10', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K81', 'K81+G', 'K81+I', 'K81+I+G', 'K81+R10', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81u', 'K81u+G', 'K81u+I', 'K81u+I+G', 'K81u+R10', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'MFP', 'SYM', 'SYM+G', 'SYM+I', 'SYM+I+G', 'SYM+R10', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'TEST', 'TIM', 'TIM+G', 'TIM+I', 'TIM+I+G', 'TIM+R10', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM2', 'TIM2+G', 'TIM2+I', 'TIM2+I+G', 'TIM2+R10', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2e', 'TIM2e+G', 'TIM2e+I', 'TIM2e+I+G', 'TIM2e+R10', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM3', 'TIM3+G', 'TIM3+I', 'TIM3+I+G', 'TIM3+R10', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3e', 'TIM3e+G', 'TIM3e+I', 'TIM3e+I+G', 'TIM3e+R10', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIMe', 'TIMe+G', 'TIMe+I', 'TIMe+I+G', 'TIMe+R10', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TN', 'TN+G', 'TN+I', 'TN+I+G', 'TN+R10', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TNe', 'TNe+G', 'TNe+I', 'TNe+I+G', 'TNe+R10', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TPM2', 'TPM2+G', 'TPM2+I', 'TPM2+I+G', 'TPM2+R10', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2u', 'TPM2u+G', 'TPM2u+I', 'TPM2u+I+G', 'TPM2u+R10', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM3', 'TPM3+G', 'TPM3+I', 'TPM3+I+G', 'TPM3+R10', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3u', 'TPM3u+G', 'TPM3u+I', 'TPM3u+I+G', 'TPM3u+R10', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TVM', 'TVM+G', 'TVM+I', 'TVM+I+G', 'TVM+R10', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVMe', 'TVMe+G', 'TVMe+I', 'TVMe+I+G', 'TVMe+R10', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9'}), optional
    Model of Nucleotide Substitution. If not provided, IQ-TREE will
    determine the best fit substitution model automatically.
n_init_pars_trees : Int % Range(1, None), optional
    Number of initial parsimony trees. If not set, program defaults will be
    used. See IQ-TREE manual for details.
n_top_init_trees : Int % Range(1, None), optional
    Number of top initial trees. If not set, program defaults will be used.
    See IQ-TREE manual for details.
n_best_retain_trees : Int % Range(1, None), optional
    Number of best trees retained during search. If not set, program
    defaults will be used. See IQ-TREE manual for details.
n_iter : Int % Range(1, None), optional
    Fix number of iterations to stop. If not set, program defaults will be
    used. See IQ-TREE manual for details.
stop_iter : Int % Range(1, None), optional
    Number of unsuccessful iterations to stop. If not set, program defaults
    will be used. See IQ-TREE manual for details.
perturb_nni_strength : Float % Range(0.01, 99), optional
    Perturbation strength for randomized NNI. If not set, program defaults
    will be used. See IQ-TREE manual for details.
spr_radius : Int % Range(1, None), optional
    Radius for parsimony SPR search. If not set, program defaults will be
    used. See IQ-TREE manual for details.
allnni : Bool, optional
    Perform more thorough NNI search.
fast : Bool, optional
    Fast search to resemble FastTree.
alrt : Int % Range(1000, None), optional
    Single branch test method. Number of bootstrap replicates to perform an
    SH-like approximate likelihood ratio test (SH-aLRT). Minimum of 1000
    replicates is recomended. Set to '0' for parametric aLRT test. Can be
    used with other 'single branch test methods'. Values reported in the
    order of: alrt, lbp, abayes.
abayes : Bool, optional
    Single branch test method. Approximate Bayes test. Can be used with
    other 'single branch test methods'. Values reported in the order of:
    alrt, lbp, abayes.
lbp : Int % Range(1000, None), optional
    Single branch test method. Number of bootstrap replicates to perform a
    fast local bootstrap probability method. Minimum of 1000 replicates is
    recomended. Can be used with other 'single branch test methods'. Values
    reported in the order of: alrt, lbp, abayes.
safe : Bool, optional
    Safe likelihood kernel to avoid numerical underflow.

Returns
-------
tree : Phylogeny[Unrooted]
    The resulting phylogenetic tree.