checkNewick {PhyloProfile} | R Documentation

## Check the validity of input newick tree

### Description

Check the validity of input newick tree

### Usage

    checkNewick(tree, inputTaxonID = NULL)

### Arguments

`tree` | input newick tree
`inputTaxonID` | list of all input taxon IDs for the phylogenetic profiles

### Value

Possible formatting error of input tree. 0 = suitable tree for using with PhyloProfile, 1 = missing parenthesis; 2 = missing comma; 3 = tree has singleton; or a list of taxa that do not exist in the input phylogenetic profile.

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`getInputTaxaID` for getting input taxon IDs, `ppTree` for an example of input tree

### Examples

    data("ppTree", package="PhyloProfile")
    checkNewick(ppTree, c("ncbi3702", "ncbi3711", "ncbi7029"))

[Package PhyloProfile version 1.2.8 Index]