PAULOWNIA is a python wrapper around [BLAST](http://blast.ncbi.nlm.nih.gov/Blast.cgi), the alignment program [MAFFT](http://mafft.cbrc.jp/alignment/software/) and the the fast neighbor-joining method implemented in [clearcut](http://bioinformatics.hungry.com/clearcut/). The purpose of the script is to efficiently add a new genome to an existing alignment, based on a set of query sequences.