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qiime2 diversity-lib beta-phylogenetic-passthrough (version 2024.10.0+q2galaxy.2024.10.0)
[required] The feature table containing the samples over which beta diversity should be computed.
[required] Phylogenetic tree containing tip identifiers that correspond to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree.
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QIIME 2: diversity-lib beta-phylogenetic-passthrough

Beta Phylogenetic Passthrough

Outputs:

distance_matrix.qza:
 The resulting distance matrix.

Description:

Computes a distance matrix for all pairs of samples in a feature table using the unifrac implementation of the selected beta diversity metric.

Examples:

run on one core (by default)

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to weighted_normalized_unifrac
  4. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza weighted-normalized-unifrac-dm.qza

to run on n cores, replace 1 here with your preferred integer

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to weighted_normalized_unifrac
  4. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza weighted-normalized-unifrac-dm.qza

use 'auto' to run on all of host system's available CPU cores

Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to weighted_normalized_unifrac
  4. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza weighted-normalized-unifrac-dm.qza

use bypass_tips to trade specificity for reduced compute time

bypass_tips can be used with any threads setting, but auto may be a good choice if you're trimming run time.
Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to weighted_normalized_unifrac
  4. Expand the additional options section
    • Set "bypass_tips" to Yes
  5. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza weighted-normalized-unifrac-dm.qza

variance adjustment

Chang et al's variance adjustment may be applied to any unifrac method by using this passthrough function.
Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to weighted_unifrac
  4. Expand the additional options section
    • Set "variance_adjusted" to Yes
  5. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza var-adj-weighted-unifrac-dm.qza

minimal generalized unifrac

Generalized unifrac is passed alpha=1 by default. This is roughly equivalent to weighted normalized unifrac, which method will be used instead, because it is better optimized.
Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to generalized_unifrac
  4. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza generalized-unifrac-dm.qza

generalized unifrac

passing a float between 0 and 1 to 'alpha' gives you control over the importance of sample proportions.
Using the qiime2 diversity-lib beta-phylogenetic-passthrough tool:
  1. Set "table" to #: feature-table.qza
  2. Set "phylogeny" to #: phylogeny.qza
  3. Set "metric" to generalized_unifrac
  4. Expand the additional options section
    • Set "alpha" to 0.75
  5. Press the Execute button.
Once completed, for the 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 diversity-lib beta-phylogenetic-passthrough [...] : distance_matrix.qza generalized-unifrac-dm.qza