Fork me on GitHub

align-to-tree-mafft-fasttree: Build a phylogenetic tree using fasttree and mafft alignmentΒΆ

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
  or ambiguously aligned will be removed (masked). The resulting masked
  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:
  --p-n-threads INTEGER   The number of threads. (Use 0 to automatically use
    Range(0, None)        all available cores) This value is used when
                          aligning the sequences and creating the tree with
                          fasttree.                               [default: 1]
  --p-mask-max-gap-frequency PROPORTION Range(0, 1, inclusive_end=True)
                          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]
  --p-mask-min-conservation PROPORTION Range(0, 1, inclusive_end=True)
                          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-masked-alignment ARTIFACT FeatureData[AlignedSequence]
                          The masked alignment.                     [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
or ambiguously aligned will be removed (masked). The resulting masked
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.

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.
masked_alignment : FeatureData[AlignedSequence]
    The masked alignment.
tree : Phylogeny[Unrooted]
    The unrooted phylogenetic tree.
rooted_tree : Phylogeny[Rooted]
    The rooted phylogenetic tree.