BeetleBase – a suite of PERL scripts to create a database of nucleotide sequences and extract user-specified single gene datasets from it.

Provided here is the collection of PERL scripts used in the manuscript: “A protocol for large-scale rRNA sequence analysis: towards a detailed phylogeny of Coleoptera” by T. Hunt and A. Vogler, Molecular and Phylogenetic Evolution (2008).

The PERL scripts contained within the accompanying folder, when used in conjuncture with each other and in combination with a selection of external programs (described below), will provide the following functions:

1. Create codenames based on the GenBank taxonomy for
   all taxonomic nodes below a user-specified start point (taxonomic group of
   interest).
2. Build a database combining these codenames and all
   available nucleotide sequences from GenBank for the taxonomic group of
   interest.
3. Aid the extraction and filtration of single gene
   datasets from the database via sequence similarity searches.
4. Produce a NEXUS format taxonomic matrix which can then be used to calculated
   the taxonomic CI/RI of phylogenetic trees (see reference for details).