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.
- 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.