SuperMatrix: creates a supermatrix from multiple gene alignments

In coleoguy/evobir: Evolutionary Biology in R

creates a supermatrix from multiple gene alignments

Description

combines all alignments in a folder into a single supermatrix

Usage

SuperMatrix(missing = "-", prefix = "concatenated", save = T,
input = "", format.in = "f", format.out = "f", concatenate = T)

Arguments

missing	the character to use when no data is available for a taxa
prefix	prefix for the resulting supermatrix
save	if True then supermatrix and partition file will be saved
input	a regular expression determining which files will be read in for example "*.fasta" will read in all files which end in ".fasta". Default is blank and will result in all files in the working directory being read in.
format.in	A character string specifying the format of the alignments to be read in. The argument is passed to read.dna in APE: "interleaved", "sequential", "clustal", or "fasta", or abbreviations of these are available.
format.out	A character string specifying the format for the supermatrix to be saved to. The argument is passed to write.dna in APE: "interleaved", "sequential", "clustal", or "fasta", or abbreviations of these are available.
concatenate	logical value when TRUE sequences are concatenated into a single fasta file. When set to FALSE sequences are saved as individual fasta files but are expanded to include all taxa in combined dataset.

Details

This function reads all alignments in the working directory and constructs a single supermatrix that includes all taxa present in any of the files and inserts missing symbols for taxa that are missing sequences for some loci.

Value

A list with two elements is returned. The first element contains partition data that records the alignment positions of each input alignment file in the combined supermatrix. The second element is a dataframe version of the supermatrix. If the argument save is set to TRUE then both of these files are also saved to the working directory.

Author(s)

Heath Blackmon

References

http://coleoguy.github.io/

Examples

## Not run: 
SuperMatrix(missing = "N", prefix = "DATASET2", save = T, format = "f")

## End(Not run)

coleoguy/evobir documentation built on May 8, 2024, 6:57 p.m.