Description Usage Arguments Details Value Author(s) References Examples
combines all alignments in a folder into a single supermatrix
1 | SuperMatrix(missing = "-", prefix = "concatenated", save = T)
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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 |
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.
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.
Heath Blackmon
1 2 3 4 | ## Not run:
SuperMatrix(missing = "N", prefix = "DATASET2", save = T)
## End(Not run)
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