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