RepeatAssembler: A Package for Annotation of Full-Length Repetitive DNA Sequences in Fungal Genomes. - Mark L. Farman; Joshua W. Gilkerson; Jerzy W. Jaromczyk; Chuck Staben (CSB, 2004)

TERMINUS - Telomeric End-Read Mining IN Unassembled Sequences. - Weixi Li; Cathryn J. Rehmeyer; Chuck Staben; Mark L. Farman (Bioinform., 2005)

TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assemblies. - Weixi Li; Cathryn J. Rehmeyer; Chuck Staben; Mark L. Farman (Bioinform., 2005)