A tool for preparing bioinformatic input for a multiple-sequence alignment.
In brief, it is written for somebody looking to run a multiple-alignment of different instances of a transposon in a genome. It uses BLAST+ to identify said instances, it assembles them into "connected" sections within the genome, and it presents them in a sort of pre-aligned version to make the multi-aligner's job easier.
This code was written for Professor Justin Blumenstiel's lab at the University of Kansas; it was designed with his constant input. The work was funded, to the best of my recollection, by a grant from the National Science Foundation. My gratitude to Prof. Blumenstiel, the NSF, and the University of Kansas for the opportunity to work on this.
This code is released under the terms of the GNU Public License version 2. See LICENSE for specific terms.