phy.names: Add information to the names in a phylip alignment file
In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

phy.names

R Documentation

Add information to the names in a phylip alignment file

Add information to the names in a phylip alignment file

phy.names(
  input.phy,
  input.csv,
  output.filename,
  separator = "_",
  prepend = TRUE,
  strict.species.names = TRUE
)

`input.phy`	A phylip-format file containing an alignment with ID names to update.
`input.csv`	A comma-separated values file with exactly two columns. This file must include a header row, but the column names are not used. The first column must include the existing ID names in the phylip alignment. The second column should contain information to be added to the alignment ID names.
`output.filename`	The file name to export. If no argument is provided to `output.filename` then the output will over-write the input in `input.phy`.
`separator`	A character string to separate the terms used in the names. This string should not be a space, since the phylip format uses spaces to distinguish names from sequence data.
`prepend`	A logical value indicating whether or not new information should be added to the beginning (TRUE, the default) or the end of the existing names.
`strict.species.names`	A logical value indicating whether or not to treat the the new information being added as a species name, and enforce a strict genus-specific epithet format (e.g. Homo sapiens neanderthalensis would become `Homo_sapiens`).