groupTips: The grouping of tree tips

In Takkoona/sitePath: Phylogeny-based sequence clustering with site polymorphism

The grouping of tree tips

Description

The tips between divergent nodes or fixation mutations on the lineages are each gathered as group.

Usage

groupTips(tree, ...)

## S3 method for class 'phyMSAmatched'
groupTips(
  tree,
  similarity = NULL,
  simMatrix = NULL,
  forbidTrivial = TRUE,
  tipnames = TRUE,
  ...
)

## S3 method for class 'lineagePath'
groupTips(tree, tipnames = TRUE, ...)

## S3 method for class 'sitesMinEntropy'
groupTips(tree, tipnames = TRUE, ...)

## S3 method for class 'fixationSites'
groupTips(tree, tipnames = TRUE, ...)

## S3 method for class 'fixationPath'
groupTips(tree, tipnames = TRUE, ...)

Arguments

tree	The return from addMSA, lineagePath, sitesMinEntropy or other functions.
...	Other arguments.
similarity	This decides how minor SNPs are to remove. If provided as fraction between 0 and 1, then the minimum number of SNP will be total tips times similariy. If provided as integer greater than 1, the minimum number will be similariy. The default similariy is 0.05 for lineagePath.
simMatrix	Deprecated and will not have effect.
forbidTrivial	Does not allow trivial trimming.
tipnames	If return tips as integer or tip names.

Value

groupTips returns grouping of tips.

Examples

data(zikv_tree)
data(zikv_align)
tree <- addMSA(zikv_tree, alignment = zikv_align)
groupTips(tree)

Takkoona/sitePath documentation built on Sept. 28, 2022, 1:24 a.m.