fas2phy: Converts FASTA files into PHYLIP format

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

Description

Converts FASTA files to a relaxed PHYLIP format.

Usage

fas2phy(file, format = "sequential", toDrop, overwrite = FALSE, ...)

Arguments

file	Character string indicating the FASTA file to convert.
format	The output format for the file: sequential or interleaved.
toDrop	Character vector indicating the names of the sequences to remove.
overwrite	If there is already a file with the same names as the output file in the working directory, should it be overwritten? (logical, default FALSE).
...	Additional arguments to be passed to

Details

Simple wrapper for ape::read.dna and ape::write.dna to facilitate file conversion. The output file gets the same name as the input file with the extension “.phy”. The function only accepts alignments (all sequences must be the same lengths). This function also allows to remove some sequences from the alignment (using their names).

Value

A logical vector indicating whether the file was created named with the name of the file.

Author(s)

Francois Michonneau

See Also

ape::write.dna

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