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Hyppo-X (download)

A topological data analysis (TDA)-based discovery tool for visual and analytical exploration of multi-dimensional phenomics data.

Citation: M. Kamruzzaman et al. arXiV preprint arXiV:1707.04362, 2017.

biLouvain  (download  

A C++ code for detecting communities in a bipartite network. There are versions of the code that can be used for strict bipartite community detection (using bipartite modularity as the objective), and for detecting communities in bipartite graphs that also have intra-type edges.

Citation: P. Pesantez, A. Kalyanaraman. IEEE TCBB, 2018, doi: 10.1109/TCBB.2017.2765319

Grappolo
(download
link1  link2)  

Photo credit: Jagain Bontha

A graph toolkit that contains multithreaded implementations for parallel graph community detection and for balanced graph coloring.

Citations: H. Lu et al. Parallel Computing, Vol. 47, pp. 19-37, 2015.
                H. Lu et al. IEEE TPDS, Vol. 28, No. 5, pp. 1240-1256, 2017.

pGraph  (download  


A parallel program to construct large-scale protein sequence homology graphs on parallel distributed and shared memory computers.

Citation: C. Wu et al. IEEE TPDS, Vol. 23, No. 10, pp. 1923-1933, 2012.

pClust  (download  


A scalable parallel software for detecting dense subgraphs (clusters) in large-scale protein sequence homology graphs (e.g., output from pGraph).

Citation: C. Wu, A. Kalyanaraman, SC'08, pp. 1-10, 2008.

LTR_seq/LTR_par  (download  


Serial and parallel software for de novo identification of full-length LTR retrotransposons (a class of genomic repeats).

Citation: A. Kalyanaraman, S. Aluru. JBCB, Vol. 4, No. 2, pp. 197-216, 2006.

PaCE  (download  


Parallel software in C/MPI for clustering large-scale Expressed Sequence Tags (or ESTs) data. This tool was developed in the early 2000s. It can also be used for modern day RNAseq/transcriptomics data clustering although it is recommended that the new generation tools be used for that purpose.

Citation: A. Kalyanaraman et al., NAR, Vol. 31, No. 11, pp. 2963-2974, 2003.