Workflow: qiime2 create phylogenetic tree

Fetched 2024-02-28 23:31:02 GMT

Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/

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Inputs

ID Type Title Doc
rooted_tree_filename String
unrooted_tree_filename String
representative_sequences File
aligned_rep_seqs_filename String
masked_aligned_rep_seqs_filename String

Steps

ID Runs Label Doc
root_tree
qiime2-step2-dada2.cwl#phylogeny-midpoint-root.cwl (CommandLineTool)
qiime2: Midpoint root an unrooted phylogenetic tree
create_tree_from_alignment
qiime2-step2-dada2.cwl#phylogeny-fasttree.cwl (CommandLineTool)
qiime2: Construct a phylogenetic tree with FastTree
mask_representative_sequences
qiime2-step2-dada2.cwl#alignment-mask.cwl (CommandLineTool)
qiime2: Mask unconserved and highly gapped columns from an alignment
align_representative_sequences
qiime2-step2-dada2.cwl#alignment-mafft.cwl (CommandLineTool)
qiime2: Perform de novo multiple sequence alignment using MAFFT

Outputs

ID Type Label Doc
rooted_tree File
unrooted_tree File
masked_representative_sequences File
aligned_representative_sequences File
Permalink: https://w3id.org/cwl/view/git/e2dc95d4f12210359360d814382e7201d836dfcf/packed/qiime2-step2-dada2.cwl?part=qiime2-05-phylogeny.cwl