qiime fragment-insertion sepp (version 2019.4)

--i-representative-sequences: ARTIFACT FeatureData[Sequence] The sequences to insert [required]:

--i-reference-alignment: ARTIFACT FeatureData[AlignedSequence] The reference multiple nucleotide alignment used to construct the reference phylogeny. [optional]:

--i-reference-phylogeny: ARTIFACT Phylogeny[Rooted] The rooted reference phylogeny. Must be in sync with reference-alignment, i.e. each tip name must have exactly one corresponding record. [optional]:

--p-alignment-subset-size: INTEGER Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time. [default: 1000]:

--p-placement-subset-size: INTEGER The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large.:

Insert fragment sequences using SEPP into reference phylogenies like Greengenes 13_8

Perform fragment insertion of 16S sequences using the SEPP algorithm against the Greengenes 13_8 99% tree.

Parameters

representative_sequences : FeatureData[Sequence]: The sequences to insert
alignment_subset_size : Int, optional: Each placement subset is further broken into subsets of at most these many sequences and a separate HMM is trained on each subset. The default alignment subset size is set to balance the exhaustiveness of the alignment step with the running time.
placement_subset_size : Int, optional: The tree is divided into subsets such that each subset includes at most these many subsets. The placement step places the fragment on only one subset, determined based on alignment scores. The default placement subset is set to make sure the memory requirement of the pplacer step does not become prohibitively large. Further reading: https://github.com/smirarab/sepp/blob/master/tutorial/sepp- tutorial.md#sample-datasets-default-parameters
reference_alignment : FeatureData[AlignedSequence], optional: The reference multiple nucleotide alignment used to construct the reference phylogeny.
reference_phylogeny : Phylogeny[Rooted], optional: The rooted reference phylogeny. Must be in sync with reference- alignment, i.e. each tip name must have exactly one corresponding record.
debug : Bool, optional: Print additional run information to STDOUT for debugging. Run together with --verbose to actually see the information on STDOUT. Temporary directories will not be removed if run fails.

Returns

tree : Phylogeny[Rooted]: The tree with inserted feature data
placements : Placements