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iqtree-ultrafast-bootstrap: Construct a phylogenetic tree with IQ-TREE with bootstrap supports.¶
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Docstring:
Usage: qiime phylogeny iqtree-ultrafast-bootstrap [OPTIONS]
Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
automatic model selection and bootstrap supports.
Inputs:
--i-alignment ARTIFACT FeatureData[AlignedSequence]
Aligned sequences to be used for phylogenetic
reconstruction. [required]
Parameters:
--p-seed INTEGER Random number seed. If not set, program defaults
will be used. See IQ-TREE manual for details.
[optional]
--p-n-cores NTHREADS The number of cores to use for parallel processing.
Use `auto` to let IQ-TREE automatically determine
the optimal number of cores to use. [default: 1]
--p-n-cores-max NTHREADS
Limits the maximum number of cores to be used when
'n-cores' is set to 'auto'. [optional]
--p-n-runs INTEGER Number of indepedent runs. Multiple independent
Range(1, None) runs (e.g. 10) can outperform a single run in terms
of likelihood maximisation. [default: 1]
--p-substitution-model TEXT Choices('JC', 'JC+I', 'JC+G', 'JC+I+G',
'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9',
'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3',
'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10',
'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4',
'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY',
'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5',
'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I',
'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6',
'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G',
'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9',
'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3',
'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10',
'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4',
'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2',
'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4',
'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10',
'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3',
'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9',
'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3',
'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9',
'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2',
'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8',
'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G',
'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7',
'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G',
'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8',
'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G',
'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7',
'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G',
'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6',
'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I',
'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5',
'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3',
'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4',
'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe',
'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4',
'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM',
'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5',
'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I',
'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6',
'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G',
'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7',
'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST')
Model of Nucleotide Substitution.If not provided,
IQ-TREE will determine the best fit substitution
model automatically. [default: 'MFP']
--p-bootstrap-replicates INTEGER
Range(1000, None) The number of bootstrap searches to perform.
Minimum of 1000 recomended. [default: 1000]
--p-n-init-pars-trees INTEGER
Range(1, None) 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(1, None) 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(1, None) Number of best trees retained during search. If not
set, program defaults will be used. See IQ-TREE
manual for details. [optional]
--p-stop-iter INTEGER Number of unsuccessful iterations to stop. If not
Range(1, None) set, program defaults will be used. See IQ-TREE
manual for details. [optional]
--p-perturb-nni-strength NUMBER
Range(0.01, 1.0) Perturbation strength for randomized NNI. If not
set, program defaults will be used. See IQ-TREE
manual for details. [optional]
--p-spr-radius INTEGER Radius for parsimony SPR search. If not set,
Range(1, None) program defaults will be used. See IQ-TREE manual
for details. [optional]
--p-n-max-ufboot-iter INTEGER
Range(1, None) Maximum number of iterations. If not set, program
defaults will be used. See IQ-TREE manual for
details. [optional]
--p-n-ufboot-steps INTEGER
Range(1, None) Number of iterations for UFBoot stopping rule. If
not set, program defaults will be used.See IQ-TREE
manual for details. [optional]
--p-min-cor-ufboot NUMBER
Range(0.51, 0.99) Minimum correlation coefficient. If not set,
program defaults will be used.See IQ-TREE manual for
details. [optional]
--p-ep-break-ufboot NUMBER
Range(0.01, 0.99) Epsilon value to break tie. 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-alrt INTEGER Single branch test method. Number of bootstrap
Range(1000, None) replicates to perform an SH-like approximate
likelihood ratio test (SH-aLRT). Minimum of 1000
replicates is required. 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. Performs an approximate
Bayes test. Can be used with other 'single branch
test methods' and ultrafast bootstrap. Values
reported in the order of: alrt, lbp, abayes, ufboot.
[default: False]
--p-lbp INTEGER Single branch test method. Number of bootstrap
Range(1000, None) replicates to perform a fast local bootstrap
probability method. Minimum of 1000 replicates is
required. Can be used with other 'single branch test
methods'. Values reported in the order of: alrt,
lbp, abayes, ufboot. [optional]
--p-bnni / --p-no-bnni Optimize UFBoot trees by NNI on bootstrap
alignment. This option reduces the risk of
overestimating branch supports with UFBoot due to
severe model violations. [default: False]
--p-safe / --p-no-safe Safe likelihood kernel to avoid numerical
underflow. [default: False]
Outputs:
--o-tree ARTIFACT The resulting phylogenetic tree.
Phylogeny[Unrooted] [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.phylogeny.methods import iqtree_ultrafast_bootstrap
Docstring:
Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
Construct a phylogenetic tree using IQ-TREE (http://www.iqtree.org/) with
automatic model selection and bootstrap supports.
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 : Threads, optional
The number of cores to use for parallel processing. Use `auto` to let
IQ-TREE automatically determine the optimal number of cores to use.
n_cores_max : Threads, optional
Limits the maximum number of cores to be used when 'n_cores' is set to
'auto'.
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('JC', 'JC+I', 'JC+G', 'JC+I+G', 'JC+R2', 'JC+R3', 'JC+R4', 'JC+R5', 'JC+R6', 'JC+R7', 'JC+R8', 'JC+R9', 'JC+R10', 'F81', 'F81+I', 'F81+G', 'F81+I+G', 'F81+R2', 'F81+R3', 'F81+R4', 'F81+R5', 'F81+R6', 'F81+R7', 'F81+R8', 'F81+R9', 'F81+R10', 'K80', 'K80+I', 'K80+G', 'K80+I+G', 'K80+R2', 'K80+R3', 'K80+R4', 'K80+R5', 'K80+R6', 'K80+R7', 'K80+R8', 'K80+R9', 'K80+R10', 'HKY', 'HKY+I', 'HKY+G', 'HKY+I+G', 'HKY+R2', 'HKY+R3', 'HKY+R4', 'HKY+R5', 'HKY+R6', 'HKY+R7', 'HKY+R8', 'HKY+R9', 'HKY+R10', 'TNe', 'TNe+I', 'TNe+G', 'TNe+I+G', 'TNe+R2', 'TNe+R3', 'TNe+R4', 'TNe+R5', 'TNe+R6', 'TNe+R7', 'TNe+R8', 'TNe+R9', 'TNe+R10', 'TN', 'TN+I', 'TN+G', 'TN+I+G', 'TN+R2', 'TN+R3', 'TN+R4', 'TN+R5', 'TN+R6', 'TN+R7', 'TN+R8', 'TN+R9', 'TN+R10', 'K81', 'K81+I', 'K81+G', 'K81+I+G', 'K81+R2', 'K81+R3', 'K81+R4', 'K81+R5', 'K81+R6', 'K81+R7', 'K81+R8', 'K81+R9', 'K81+R10', 'K81u', 'K81u+I', 'K81u+G', 'K81u+I+G', 'K81u+R2', 'K81u+R3', 'K81u+R4', 'K81u+R5', 'K81u+R6', 'K81u+R7', 'K81u+R8', 'K81u+R9', 'K81u+R10', 'TPM2', 'TPM2+I', 'TPM2+G', 'TPM2+I+G', 'TPM2+R2', 'TPM2+R3', 'TPM2+R4', 'TPM2+R5', 'TPM2+R6', 'TPM2+R7', 'TPM2+R8', 'TPM2+R9', 'TPM2+R10', 'TPM2u', 'TPM2u+I', 'TPM2u+G', 'TPM2u+I+G', 'TPM2u+R2', 'TPM2u+R3', 'TPM2u+R4', 'TPM2u+R5', 'TPM2u+R6', 'TPM2u+R7', 'TPM2u+R8', 'TPM2u+R9', 'TPM2u+R10', 'TPM3', 'TPM3+I', 'TPM3+G', 'TPM3+I+G', 'TPM3+R2', 'TPM3+R3', 'TPM3+R4', 'TPM3+R5', 'TPM3+R6', 'TPM3+R7', 'TPM3+R8', 'TPM3+R9', 'TPM3+R10', 'TPM3u', 'TPM3u+I', 'TPM3u+G', 'TPM3u+I+G', 'TPM3u+R2', 'TPM3u+R3', 'TPM3u+R4', 'TPM3u+R5', 'TPM3u+R6', 'TPM3u+R7', 'TPM3u+R8', 'TPM3u+R9', 'TPM3u+R10', 'TIMe', 'TIMe+I', 'TIMe+G', 'TIMe+I+G', 'TIMe+R2', 'TIMe+R3', 'TIMe+R4', 'TIMe+R5', 'TIMe+R6', 'TIMe+R7', 'TIMe+R8', 'TIMe+R9', 'TIMe+R10', 'TIM', 'TIM+I', 'TIM+G', 'TIM+I+G', 'TIM+R2', 'TIM+R3', 'TIM+R4', 'TIM+R5', 'TIM+R6', 'TIM+R7', 'TIM+R8', 'TIM+R9', 'TIM+R10', 'TIM2e', 'TIM2e+I', 'TIM2e+G', 'TIM2e+I+G', 'TIM2e+R2', 'TIM2e+R3', 'TIM2e+R4', 'TIM2e+R5', 'TIM2e+R6', 'TIM2e+R7', 'TIM2e+R8', 'TIM2e+R9', 'TIM2e+R10', 'TIM2', 'TIM2+I', 'TIM2+G', 'TIM2+I+G', 'TIM2+R2', 'TIM2+R3', 'TIM2+R4', 'TIM2+R5', 'TIM2+R6', 'TIM2+R7', 'TIM2+R8', 'TIM2+R9', 'TIM2+R10', 'TIM3e', 'TIM3e+I', 'TIM3e+G', 'TIM3e+I+G', 'TIM3e+R2', 'TIM3e+R3', 'TIM3e+R4', 'TIM3e+R5', 'TIM3e+R6', 'TIM3e+R7', 'TIM3e+R8', 'TIM3e+R9', 'TIM3e+R10', 'TIM3', 'TIM3+I', 'TIM3+G', 'TIM3+I+G', 'TIM3+R2', 'TIM3+R3', 'TIM3+R4', 'TIM3+R5', 'TIM3+R6', 'TIM3+R7', 'TIM3+R8', 'TIM3+R9', 'TIM3+R10', 'TVMe', 'TVMe+I', 'TVMe+G', 'TVMe+I+G', 'TVMe+R2', 'TVMe+R3', 'TVMe+R4', 'TVMe+R5', 'TVMe+R6', 'TVMe+R7', 'TVMe+R8', 'TVMe+R9', 'TVMe+R10', 'TVM', 'TVM+I', 'TVM+G', 'TVM+I+G', 'TVM+R2', 'TVM+R3', 'TVM+R4', 'TVM+R5', 'TVM+R6', 'TVM+R7', 'TVM+R8', 'TVM+R9', 'TVM+R10', 'SYM', 'SYM+I', 'SYM+G', 'SYM+I+G', 'SYM+R2', 'SYM+R3', 'SYM+R4', 'SYM+R5', 'SYM+R6', 'SYM+R7', 'SYM+R8', 'SYM+R9', 'SYM+R10', 'GTR', 'GTR+I', 'GTR+G', 'GTR+I+G', 'GTR+R2', 'GTR+R3', 'GTR+R4', 'GTR+R5', 'GTR+R6', 'GTR+R7', 'GTR+R8', 'GTR+R9', 'GTR+R10', 'MFP', 'TEST'), optional
Model of Nucleotide Substitution.If not provided, IQ-TREE will
determine the best fit substitution model automatically.
bootstrap_replicates : Int % Range(1000, None), optional
The number of bootstrap searches to perform. Minimum of 1000
recomended.
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.
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, 1.0), 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.
n_max_ufboot_iter : Int % Range(1, None), optional
Maximum number of iterations. If not set, program defaults will be
used. See IQ-TREE manual for details.
n_ufboot_steps : Int % Range(1, None), optional
Number of iterations for UFBoot stopping rule. If not set, program
defaults will be used.See IQ-TREE manual for details.
min_cor_ufboot : Float % Range(0.51, 0.99), optional
Minimum correlation coefficient. If not set, program defaults will be
used.See IQ-TREE manual for details.
ep_break_ufboot : Float % Range(0.01, 0.99), optional
Epsilon value to break tie. If not set, program defaults will be used.
See IQ-TREE manual for details.
allnni : Bool, optional
Perform more thorough NNI search.
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 required. 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. Performs an approximate Bayes test. Can be
used with other 'single branch test methods' and ultrafast bootstrap.
Values reported in the order of: alrt, lbp, abayes, ufboot.
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
required. Can be used with other 'single branch test methods'. Values
reported in the order of: alrt, lbp, abayes, ufboot.
bnni : Bool, optional
Optimize UFBoot trees by NNI on bootstrap alignment. This option
reduces the risk of overestimating branch supports with UFBoot due to
severe model violations.
safe : Bool, optional
Safe likelihood kernel to avoid numerical underflow.
Returns
-------
tree : Phylogeny[Unrooted]
The resulting phylogenetic tree.