The paper describing a software package I created with Jennifer H. Wisecaver (now at Vanderbilt University) while we were both PhD students at the University of Arizona has been accepted for publication in the journal PeerJ. Even as a preprint on arXiv it was cited multiple times (included by papers in Nature Communications and PNAS).
The application SiClE (for Sister Clade Extractor) was created to perform high-throughput phylogenetic analysis. Given a tree and a search term it first determines if the search term is monophyletic in the tree then identifies the two sister clades. It has been used successfully as an initial filtering step to investigate horizontal gene transfer at the high-throughput scale. The program is open source and freely available under a Creative Commons License at http://eebweb.arizona.edu/sicle/.
Read the paper at https://peerj.com/articles/2359/.