# align-to-tree-mafft-raxml: Build a phylogenetic tree using raxml and mafft alignment.¶

#### Docstring:

Usage: qiime phylogeny align-to-tree-mafft-raxml [OPTIONS]

This pipeline will start by creating a sequence alignment using MAFFT,
after which any alignment columns that are phylogenetically uninformative
alignment will be used to infer a phylogenetic tree using RAxML, under the
specified substitution model, and then subsequently rooted at its
midpoint. Output files from each step of the pipeline will be saved. This
methods, and both the rooted and unrooted phylogenies from q2-phylogeny
methods.

Inputs:
--i-sequences ARTIFACT FeatureData[Sequence]
The sequences to be used for creating a iqtree
based rooted phylogenetic tree.           [required]
Parameters:
--p-n-threads VALUE Int % Range(1, None) | Str % Choices('auto')
The number of threads. (Use all to automatically
use all available cores. This value is used when
aligning the sequences and creating the tree with
iqtree.                                 [default: 1]
The maximum relative frequency of gap characters in
a column for the column to be retained. This
relative frequency must be a number between 0.0 and
1.0 (inclusive), where 0.0 retains only those
columns without gap characters, and 1.0 retains all
columns  regardless of gap character frequency. This
value is used when masking the aligned sequences.
[default: 1.0]
The minimum relative frequency of at least one
non-gap character in a column for that column to be
retained. This relative frequency must be a number
between 0.0 and 1.0 (inclusive). For example, if a
value of  0.4 is provided, a column will only be
retained  if it contains at least one character that
is present in at least 40% of the sequences. This
value is used when masking the aligned sequences.
[default: 0.4]
--p-parttree / --p-no-parttree
This flag is required if the number of sequences
being aligned are larger than 1000000. Disabled by
default. NOTE: if using this option, it is
recomended that only the CAT-based substitution
models of RAxML be considered for this pipeline.
[default: False]
--p-substitution-model TEXT Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT',
'GTRCATI')            Model of Nucleotide Substitution.
[default: 'GTRGAMMA']
--p-seed INTEGER        Random number seed for the parsimony starting tree.
This allows you to reproduce tree results. If not
supplied then one will be randomly chosen.
[optional]
--p-raxml-version TEXT Choices('Standard', 'SSE3', 'AVX2')
Select a specific CPU optimization of RAxML to use.
The SSE3 versions will run approximately 40% faster
than the standard version. The AVX2 version will run
10-30% faster than the SSE3 version.
[default: 'Standard']
Outputs:
--o-alignment ARTIFACT FeatureData[AlignedSequence]
The aligned sequences.                    [required]
--o-tree ARTIFACT       The unrooted phylogenetic tree.
Phylogeny[Unrooted]                                             [required]
--o-rooted-tree ARTIFACT
Phylogeny[Rooted]     The rooted phylogenetic tree.             [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).
--examples              Show usage examples and exit.
--citations             Show citations and exit.
--help                  Show this message and exit.

#### Import:

from qiime2.plugins.phylogeny.pipelines import align_to_tree_mafft_raxml


#### Docstring:

Build a phylogenetic tree using raxml and mafft alignment.

This pipeline will start by creating a sequence alignment using MAFFT,
after which any alignment columns that are phylogenetically uninformative
alignment will be used to infer a phylogenetic tree using RAxML, under the
specified substitution model, and then subsequently rooted at its midpoint.
Output files from each step of the pipeline will be saved. This includes
both the rooted and unrooted phylogenies from q2-phylogeny methods.

Parameters
----------
sequences : FeatureData[Sequence]
The sequences to be used for creating a iqtree based rooted
phylogenetic tree.
n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
The number of threads. (Use all to automatically use all available
cores. This value is used when aligning the sequences and creating the
tree with iqtree.
mask_max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
The maximum relative frequency of gap characters in a column for the
column to be retained. This relative frequency must be a number between
0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
gap characters, and 1.0 retains all columns  regardless of gap
character frequency. This value is used when masking the aligned
sequences.
mask_min_conservation : Float % Range(0, 1, inclusive_end=True), optional
The minimum relative frequency of at least one non-gap character in a
column for that column to be retained. This relative frequency must be
a number between 0.0 and 1.0 (inclusive). For example, if a value of
0.4 is provided, a column will only be retained  if it contains at
least one character that is present in at least 40% of the sequences.
This value is used when masking the aligned sequences.
parttree : Bool, optional
This flag is required if the number of sequences being aligned are
larger than 1000000. Disabled by default. NOTE: if using this option,
it is recomended that only the CAT-based substitution models of RAxML
be considered for this pipeline.
substitution_model : Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI'), optional
Model of Nucleotide Substitution.
seed : Int, optional
Random number seed for the parsimony starting tree. This allows you to
reproduce tree results. If not supplied then one will be randomly
chosen.
raxml_version : Str % Choices('Standard', 'SSE3', 'AVX2'), optional
Select a specific CPU optimization of RAxML to use. The SSE3 versions
will run approximately 40% faster than the standard version. The AVX2
version will run 10-30% faster than the SSE3 version.

Returns
-------
alignment : FeatureData[AlignedSequence]
The aligned sequences.
The rooted phylogenetic tree.