Phylogenetic tree construction

Phylogenetic tree construction#

In this chapter we’ll continue our efforts to annotate the features we observed in this study, this time by building a phylogenetic tree from the seqeunces. This will provide information that we’ll use later to approximately quantify the evolutionary relationships between the feature sequences that we observed.

Aligning sequences and building a phylogenetic tree#

We’ll build a phylogenetic tree from our ASV sequences using the q2-phylogeny plugin’s align_to_tree_mafft_fasttree action. This action is a pipeline in QIIME 2, which means that it strings together multiple simpler operations that are often performed together to reduce the number of steps that users have to take. Pipelines are used in the same way as other actions.

This particular pipeline performs four distinct steps steps:

  1. perform a multiple sequence alignment using mafft

  2. filter highly variable positions from the alignment (these positions tend to introduce noise into the phylogenetic tree)

  3. build an unrooted phylogenetic tree

  4. add a root to the unrooted tree

The final unrooted phylogenetic tree will be used for analyses that we perform next - specifically for computing phylogenetically aware diversity metrics. While output artifacts will be available for each of these steps, we’ll only use the rooted phylogenetic tree later.

import qiime2.plugins.phylogeny.actions as phylogeny_actions

action_results = phylogeny_actions.align_to_tree_mafft_fasttree(
    sequences=filtered_sequences_2,
)
aligned_rep_seqs = action_results.alignment
masked_aligned_rep_seqs = action_results.masked_alignment
unrooted_tree = action_results.tree
rooted_tree = action_results.rooted_tree

phylogeny_actions <- import("qiime2.plugins.phylogeny.actions")

action_results <- phylogeny_actions$align_to_tree_mafft_fasttree(
    sequences=filtered_sequences_2,
)
aligned_rep_seqs <- action_results$alignment
masked_aligned_rep_seqs <- action_results$masked_alignment
unrooted_tree <- action_results$tree
rooted_tree <- action_results$rooted_tree

qiime phylogeny align-to-tree-mafft-fasttree \
  --i-sequences filtered-sequences-2.qza \
  --output-dir phylogeny-align-to-tree-mafft-fasttree

_, _, _, rooted_tree = use.action(
    use.UsageAction(plugin_id='phylogeny',
                    action_id='align_to_tree_mafft_fasttree'),
    use.UsageInputs(sequences=filtered_sequences_2),
    use.UsageOutputNames(alignment='aligned_rep_seqs',
                         masked_alignment='masked_aligned_rep_seqs',
                         tree='unrooted_tree', rooted_tree='rooted_tree'),
)
Using the qiime2 phylogeny align-to-tree-mafft-fasttree tool:

  1. Set “sequences” to #: filtered-sequences-2.qza

  2. Press the Execute button.

Once completed, for each new entry in your history, use the Edit button to set the name as follows:

(Renaming is optional, but it will make any subsequent steps easier to complete.)

History Name

“Name” to set (be sure to press Save)

#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : alignment.qza

aligned-rep-seqs.qza

#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : masked_alignment.qza

masked-aligned-rep-seqs.qza

#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : tree.qza

unrooted-tree.qza

#: qiime2 phylogeny align-to-tree-mafft-fasttree [...] : rooted_tree.qza

rooted-tree.qza

  • phylogeny-align-to-tree-mafft-fasttree/alignment.qza | view | download

  • phylogeny-align-to-tree-mafft-fasttree/masked_alignment.qza | view | download

  • phylogeny-align-to-tree-mafft-fasttree/tree.qza | view | download

  • phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza | view | download

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