Ananth Kalyanaraman

Associate Professor
School of EECS
Washington State University

OPEN SOURCE SOFTWARE

biLouvain (download): A C++ implementation of our biLouvain algorithm for community detection in bipartite graphs.
Citation: P. Pesantez, A. Kalyanaraman. Detecting communities in biological bipartite networks. Proc. ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), October 2-5, 2016, Seattle, WA.

Grappolo (download): Multithreaded software for community detection in large graphs.
Citation: H. Lu, M. Halappanavar, A. Kalyanaraman. Parallel heuristics for scalable community detection. Parallel Computing, Vol. 47, pp. 19-37, 2015.

PaCE (email request): Parallel software for clustering DNA (transcriptomic/cDNA/EST/RNAseq) sequences. Developed as part of my doctoral dissertation (Kalyanaraman et al., JPDC 2007, NAR 2003, TPDS 2003)

LTR_par/LTR_seq (email request): 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 eitherananth@eecs.wsu.edu or aluru@iastate.edu. (A. Kalyanaraman, S. Aluru, JBCB 2006).

pGraph (download):    Parallel construction of large-scale protein sequence homology graphs   (Wu, Kalyanaraman and Cannon, ICPP 2010, TPDS 2012). A more scalable version of the software (pGraph-Tascel - Daily et al. JPDC 2015)  is available by email request.

pClust (download):    Parallel identification of dense protein clusters (Wu and Kalyanaraman, SC'08)

MR-MSPolygraph (download):    A MapReduce implementation of a hybrid spectral library-database search method for peptide identification (Kalyanaraman et al., Bioinformatics 2011)