raxmlPartitionCreate: Create a RAxML-formatted partition file

In fmichonneau/chopper: Alignment Manipulations and Data Preparation for Phylogenetic Analyses

Description

Given a PHYLIP file, this function returns a RAxML formatted partition file that is split by codon position.

Usage

raxmlPartitionCreate(raxmlAlg, file.out = "raxml_partition",
  part.names = c("p1", "p2", "p3"), overwrite = FALSE)

Arguments

raxmlAlg	The path to a PHYLIP formatted file
file.out	The file name and path to the output file
part.names	The names of the partitions used, the length of this arguments determines how many partitions are generated. By default 3, making one partition per codon position.
overwrite	If a file with the same name as file.out exists, should it be overwritten? (default FALSE.

Details

By default the number of partitions is determined by how many names are provided.

The file used (supplied with raxmlAlg) must be a PHYLIP formatted file: the first line must contain the number of sequences, followed by the length of the sequences.

Value

a named logical vector indicating whether the file was created.

Author(s)

Francois Michonneau

fmichonneau/chopper documentation built on May 16, 2019, 1:43 p.m.