q2-phylogeny

qiime2

This QIIME 2 plugin supports generating and manipulating phylogenetic trees.

version: 2024.10.0
website: https://github.com/qiime2/q2-phylogeny
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Name	Type	Short Description
midpoint-root	method	Midpoint root an unrooted phylogenetic tree.
fasttree	method	Construct a phylogenetic tree with FastTree.
raxml	method	Construct a phylogenetic tree with RAxML.
raxml-rapid-bootstrap	method	Construct a phylogenetic tree with bootstrap supports using RAxML.
iqtree	method	Construct a phylogenetic tree with IQ-TREE.
iqtree-ultrafast-bootstrap	method	Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
filter-table	method	Remove features from table if they're not present in tree.
filter-tree	method	Remove features from tree based on metadata
robinson-foulds	method	Calculate Robinson-Foulds distance between phylogenetic trees.
align-to-tree-mafft-fasttree	pipeline	Build a phylogenetic tree using fasttree and mafft alignment
align-to-tree-mafft-iqtree	pipeline	Build a phylogenetic tree using iqtree and mafft alignment.
align-to-tree-mafft-raxml	pipeline	Build a phylogenetic tree using raxml and mafft alignment.

This QIIME 2 plugin supports generating and manipulating phylogenetic trees.

version: 2024.10.0
website: https://github.com/qiime2/q2-phylogeny
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Name	Type	Short Description
midpoint-root	method	Midpoint root an unrooted phylogenetic tree.
fasttree	method	Construct a phylogenetic tree with FastTree.
raxml	method	Construct a phylogenetic tree with RAxML.
raxml-rapid-bootstrap	method	Construct a phylogenetic tree with bootstrap supports using RAxML.
iqtree	method	Construct a phylogenetic tree with IQ-TREE.
iqtree-ultrafast-bootstrap	method	Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
filter-table	method	Remove features from table if they're not present in tree.
filter-tree	method	Remove features from tree based on metadata
robinson-foulds	method	Calculate Robinson-Foulds distance between phylogenetic trees.
align-to-tree-mafft-fasttree	pipeline	Build a phylogenetic tree using fasttree and mafft alignment
align-to-tree-mafft-iqtree	pipeline	Build a phylogenetic tree using iqtree and mafft alignment.
align-to-tree-mafft-raxml	pipeline	Build a phylogenetic tree using raxml and mafft alignment.

This QIIME 2 plugin supports generating and manipulating phylogenetic trees.

version: 2024.10.0
website: https://github.com/qiime2/q2-phylogeny
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Name	Type	Short Description
midpoint-root	method	Midpoint root an unrooted phylogenetic tree.
fasttree	method	Construct a phylogenetic tree with FastTree.
raxml	method	Construct a phylogenetic tree with RAxML.
raxml-rapid-bootstrap	method	Construct a phylogenetic tree with bootstrap supports using RAxML.
iqtree	method	Construct a phylogenetic tree with IQ-TREE.
iqtree-ultrafast-bootstrap	method	Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
filter-table	method	Remove features from table if they're not present in tree.
filter-tree	method	Remove features from tree based on metadata
robinson-foulds	method	Calculate Robinson-Foulds distance between phylogenetic trees.
align-to-tree-mafft-fasttree	pipeline	Build a phylogenetic tree using fasttree and mafft alignment
align-to-tree-mafft-iqtree	pipeline	Build a phylogenetic tree using iqtree and mafft alignment.
align-to-tree-mafft-raxml	pipeline	Build a phylogenetic tree using raxml and mafft alignment.

This QIIME 2 plugin supports generating and manipulating phylogenetic trees.

version: 2024.10.0
website: https://github.com/qiime2/q2-phylogeny
user support:: Please post to the QIIME 2 forum for help with this plugin: https://forum.qiime2.org

Name	Type	Short Description
midpoint-root	method	Midpoint root an unrooted phylogenetic tree.
fasttree	method	Construct a phylogenetic tree with FastTree.
raxml	method	Construct a phylogenetic tree with RAxML.
raxml-rapid-bootstrap	method	Construct a phylogenetic tree with bootstrap supports using RAxML.
iqtree	method	Construct a phylogenetic tree with IQ-TREE.
iqtree-ultrafast-bootstrap	method	Construct a phylogenetic tree with IQ-TREE with bootstrap supports.
filter-table	method	Remove features from table if they're not present in tree.
filter-tree	method	Remove features from tree based on metadata
robinson-foulds	method	Calculate Robinson-Foulds distance between phylogenetic trees.
align-to-tree-mafft-fasttree	pipeline	Build a phylogenetic tree using fasttree and mafft alignment
align-to-tree-mafft-iqtree	pipeline	Build a phylogenetic tree using iqtree and mafft alignment.
align-to-tree-mafft-raxml	pipeline	Build a phylogenetic tree using raxml and mafft alignment.

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