R: Read phylogenetic trees from files

read_nexus_phylo {rncl} | R Documentation

## Read phylogenetic trees from files

### Description

Create phylo objects from NEXUS or Newick files

### Usage

    read_nexus_phylo(file, simplify = FALSE, missing_edge_length = NA,
      show_progress = TRUE, ...)

    read_newick_phylo(file, simplify = FALSE, missing_edge_length = NA,
      show_progress = TRUE, ...)

    make_phylo(file, simplify = FALSE, missing_edge_length = NA, ...)

### Arguments

`file` | Path of NEXUS or Newick file
`simplify` | If the file includes more than one tree, returns only the first tree; otherwise, returns a multiPhylo object
`missing_edge_length` | If the tree contains missing edge lengths, the value to be attributed to these edge lengths. By default, (`missing_edge_length = NA`) if at least edge length is missing, they are all removed. Otherwise, the value must be a single numeric value. In any case, a warning will be generated if the tree contains missing edge lengths.
`show_progress` | If `TRUE` (default)), a progress bar is displayed during the possibly time consuming step of removing the singletons from the tree.
`...` | additional parameters to be passed to the rncl function

### Details

These functions read NEXUS or Newick files and return an object of class phylo/multiPhylo.

### Value

A phylo or a multiPhylo object

### Note

`make_phylo` will soon be deprecated, use `read_nexus_phylo` or `read_newick_phylo` instead.

### Author(s)

Francois Michonneau

### See Also

rncl-package

[Package rncl version 0.8.3 Index]