SuperMatrix {evobiR}

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)

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

Details

This function reads all fasta format alignments in the working directory and constructs a single supermatrix that includes all taxa present in any of the fasta 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 fasta 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)

## End(Not run)