SOFTWARE
PaCE:
Parallel software for clustering DNA sequences. Developed as part of my doctoral dissertation. The official website of the software is: http://www.ee.iastate.edu/~aluru/software/PaCE/index.html.
Citation:
(2003) A. Kalyanaraman, S. Aluru, V. Brendel, S. Kothari. Space and time efficient parallel algorithms and software for EST clustering. IEEE Transactions on Parallel and Distributed Systems (TPDS), 14(12):1209-1221.
(2003) A. Kalyanaraman, S. Aluru, S. Kothari, V. Brendel. Efficient clustering of large EST data sets on parallel computers. Nucleic Acids Research (NAR), 31(11):2963-2974.
LTR_par:
Serial and parallel software for de novo identification of full-length LTR retrotransposons (a class of genomic repeats) in genomes. Developed as part of my doctoral dissertation. The software is free for academic and non-profit licensing, and can be acquired by sending an email to either ananth@eecs.wsu.edu or aluru@iastate.edu.
Citation:
(2006) A. Kalyanaraman, S. Aluru. Efficient algorithms and software for detection of full-length LTR retrotransposons. Journal of Bioinformatics and Computational Biology (JBCB), 4(2):197-216.