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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.

Options:
  --i-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The sequences to be used for creating a
                                  fasttree based rooted phylogenetic tree.
                                  [required]
  --p-n-threads INTEGER RANGE     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.
                                  [default: 1]
  --p-mask-max-gap-frequency FLOAT
                                  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 FLOAT
                                  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]
  --o-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  The aligned sequences.  [required if not
                                  passing --output-dir]
  --o-masked-alignment ARTIFACT PATH FeatureData[AlignedSequence]
                                  The masked alignment.  [required if not
                                  passing --output-dir]
  --o-tree ARTIFACT PATH Phylogeny[Unrooted]
                                  The unrooted phylogenetic tree.  [required
                                  if not passing --output-dir]
  --o-rooted-tree ARTIFACT PATH Phylogeny[Rooted]
                                  The rooted 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.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.