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
  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 VALUE Int % Range(1, None) | Str % Choices('auto')
                          The number of threads. (Use `auto` 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 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]
  --p-parttree / --p-no-parttree
                          This flag is required if the number of sequences
                          being aligned are larger than 1000000. Disabled by
                          default.                            [default: False]
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).
  --example-data PATH     Write example data and exit.
  --citations             Show citations and exit.
  --help                  Show this message and exit.