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

#### Docstring:

Usage: qiime phylogeny align-to-tree-mafft-fasttree [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 and then subsequently
rooted at its midpoint. Output files from each step of the pipeline will
be saved. This includes both the unmasked and masked MAFFT alignment from
q2-alignment 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 fasttree
based rooted phylogenetic tree.           [required]
Parameters:
Range(0, None)        all available cores) This value is used when
aligning the sequences and creating the tree with
fasttree.                               [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]
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).
--citations             Show citations and exit.
--help                  Show this message and exit.

#### Import:

from qiime2.plugins.phylogeny.pipelines import align_to_tree_mafft_fasttree


#### Docstring:

Build a phylogenetic tree using fasttree 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 and then subsequently
rooted at its midpoint. Output files from each step of the pipeline will be
q2-alignment methods, and both the rooted and unrooted phylogenies from
q2-phylogeny methods.

Parameters
----------
sequences : FeatureData[Sequence]
The sequences to be used for creating a fasttree based rooted
phylogenetic tree.
n_threads : Int % Range(0, None), optional
The number of threads. (Use 0 to automatically use all available cores)
This value is used when aligning the sequences and creating the tree
with fasttree.
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.

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