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