treemer {sitePath} | R Documentation

## Topology-dependent tree trimming

### Description

`groupTips` uses sequence similarity to group tree tips. Members in a group are always constrained to share the same ancestral node. Similarity between two tips is derived from their multiple sequence alignment. The site will not be counted into total length if both are gap. Similarity is calculated as number of matched divided by the corrected total length. So far the detection of divergence is based on one simple rule: the miminal pairwise similarity. The two branches are decided to be divergent if the similarity is lower than the threshold. (Other more statistical approaches such as Kolmogorov-Smirnov Tests among pair-wise distance could be introduced in the future)

`lineagePath` finds the lineages of a phylogenetic tree providing the corresponding sequence alignment. This is done by finding 'major SNPs' which usually accumulate along the evolutionary pathways. are added.

### Usage

    groupTips(
      tree,
      similarity = NULL,
      simMatrix = NULL,
      forbidTrivial = TRUE,
      tipnames = TRUE
    )

    lineagePath(tree, similarity = NULL, simMatrix = NULL, forbidTrivial = TRUE)

### Arguments

`tree` | The return from `addMSA` function
`similarity` | Similarity threshold for tree trimming in `groupTips`. If not provided, the mean similarity substract standard deviation of all sequences will be used. And for `lineagePath`, 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 0.1 for `lineagePath`.
`simMatrix` | A diagonal matrix of similarities for each pair of sequences. This parameter will not have effect in the function `lineagePath`.
`forbidTrivial` | Does not allow trivial trimming
`tipnames` | If return as tipnames

### Value

grouping of tips

path represent by node number

### Examples

    data('zikv_tree')
    data('zikv_align')
    tree <- addMSA(zikv_tree, alignment = zikv_align)
    groupTips(tree, 0.996)
    lineagePath(tree)

[Package sitePath version 1.4.2 Index]