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Tools for working with taxonomic names
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matchnames
parsenames

README.md

taxon-tools

Tools for working with taxonomic names

Tools

matchnames

Reconciling small variations in taxonomic names facilitates the integration of biological names-based data. This tool matches a query list of (parsed) taxonomic names (List A) against a reference list (List B), according to a set of taxonomic rules (described below). The taxonomic rules are most appropriate for plant names, as specified by the International Code of Botanical Nomenclature. Can also perform approximate (fuzzy) matching to identify variations (e.g., misspelling) in binomial names and author strings. An output status code is given for each type of match.

See the man page for more details.

parsenames

Split biological names into component parts:

  1. Genus hybrid sign
  2. Genus name
  3. Species hybrid sign
  4. Specific epithet
  5. Infraspecific rank signifier (“subsp.”, “var.”, etc.)
  6. Infraspecific epithet
  7. Name’s author string

Most of the work is done by a single regular expression. See the man page for more details.

Install

All tools are AWK scripts for use with the Gawk flavor of AWK. matchnames uses the aregex Gawk extension. Before installing matchnames the aregex.so file must be present in a directory in $AWKLIBPATH (of both user and root).

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