similarity_tree: Similarity tree
In irycisBioinfo/PATO: Pangenome Analysis Toolkit
View source: R/similarity_tree.R
similarity_tree R Documentation
Similarity tree
Description
Build a similarity tree (pseudo-phylogenetic) of the samples,
using whole-genome (mash) or accessory genome (accnet).
Usage
similarity_tree(data, method = "NJ")
Arguments
data
An accnet or mash object.
method
Tree method c("fastme", "NJ", "UPGMA"):
fastme: Tree Estimation Based on the Minimum Evolution Algorithm
NJ: Neighbor-Joining Tree Estimation
UPGMA: Unweighted pair group method with arithmetic mean
ward.D2: Ward's minimum variance metho
median: WPGMC Weighted Pair Group Method with Arithmetic Mean
complete: complete linkage
Value
An object of class phylo
See Also
fastme
nj
hclust
irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.
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View source: R/similarity_tree.R
| similarity_tree | R Documentation |
Similarity tree
Description
Build a similarity tree (pseudo-phylogenetic) of the samples, using whole-genome (mash) or accessory genome (accnet).
Usage
similarity_tree(data, method = "NJ")
Arguments
data |
An accnet or mash object. |
method |
Tree method c("fastme", "NJ", "UPGMA"):
|
Value
An object of class phylo
See Also
fastme
nj
hclust
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.
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