extend.tree: Place new sequences on the tree. This function makes calls to...
In PoonLab/clustuneR: Molecular clustering implementation and predictive optimization
extend.tree R Documentation
Place new sequences on the tree.
This function makes calls to pplacer and guppy binaries (Matsen, 2010)
provided with this package. pplacer ensures that previously defined clusters
remain the same. New tips are assigned a set of possible placements in the
tree.
Description
Place new sequences on the tree.
This function makes calls to pplacer and guppy binaries (Matsen, 2010)
provided with this package. pplacer ensures that previously defined clusters
remain the same. New tips are assigned a set of possible placements in the
tree.
Usage
extend.tree(phy, seqs.full, log.file = NA, locus = "LOCUS")
Arguments
phy:
ape::phylo object. Must be annotated with seq.info, node.info,
and path.info by calling import.tree().
seqs.full:
ape::DNAbin or AAbin object. This sequence alignment
must contain all known sequences in the tree phy, as
well as all new sequences we want to graft to the tree
as potential cluster growth.
log.file:
character. A path to the logfile from a tree reconstruction
run. This file can be produced by IQTREE, FastTree or RAxML.
Value
ape::phylo object with growth.info field
PoonLab/clustuneR documentation built on Jan. 29, 2024, 2:40 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
| extend.tree | R Documentation |
Place new sequences on the tree. This function makes calls to pplacer and guppy binaries (Matsen, 2010) provided with this package. pplacer ensures that previously defined clusters remain the same. New tips are assigned a set of possible placements in the tree.
Description
Place new sequences on the tree. This function makes calls to pplacer and guppy binaries (Matsen, 2010) provided with this package. pplacer ensures that previously defined clusters remain the same. New tips are assigned a set of possible placements in the tree.
Usage
extend.tree(phy, seqs.full, log.file = NA, locus = "LOCUS")
Arguments
phy: |
ape::phylo object. Must be annotated with seq.info, node.info, and path.info by calling import.tree(). |
seqs.full: |
ape::DNAbin or AAbin object. This sequence alignment
must contain all known sequences in the tree |
log.file: |
character. A path to the logfile from a tree reconstruction run. This file can be produced by IQTREE, FastTree or RAxML. |
Value
ape::phylo object with growth.info field
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.