OPEN SOURCE SOFTWARE
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.
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.
(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 firstname.lastname@example.org or email@example.com. (A. Kalyanaraman, S. Aluru, JBCB 2006).
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
pClust (download): Parallel identification of dense protein clusters (Wu and Kalyanaraman, SC'08)
A MapReduce implementation of a hybrid spectral library-database
search method for peptide identification (Kalyanaraman et al.,