OPEN SOURCE SOFTWARE
Grappolo (download): Multithreaded software for community detection in large graphs (Lu et al. ParCo 2015). Parallel implementation of the Louvain heuristic.
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 email@example.com or firstname.lastname@example.org. (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.,