Ananth Kalyanaraman

Associate Professor
School of EECS
Washington State University


Hyppo-X (download): A topological data analysis-based discovery tool for semi-automated hypothesis extraction from high-dimensional phenomics data.
Authors: M. Kamruzzaman, A. Kalyanaraman, B. Krishnamoorthy, P.S. Schnable.
Toward a scalable framework for complex high-dimensional phenomics data. arXiV preprint arXiV:1707.04362, 2017.

Interesting paths in Mapper. arXiV preprint arXiV:1712.10197, 2017.

Grappolo-TK (download): Graph toolkit that contains multithreaded implementations for graph community detection and balanced coloring.
H. Lu, M. Halappanavar, A. Kalyanaraman. Parallel heuristics for scalable community detection. Parallel Computing, Vol. 47, pp. 19-37, 2015.
H. Lu, M. Halappanvar, D. Chavarria-Miranda, A. Gebremedhin, A. Panyala, A. Kalyanaraman. Algorithms for balanced graph colorings with applications in parallel computing. IEEE Transactions on Parallel and Distributed Systems, Vol. 28, No. 5, pp. 1240-1256, May 1 2017.

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.

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 or (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)