ZENBU developed by Jessica Severin.
Please cite this paper to refer to ZENBU:
Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y; FANTOM Consortium, Bertin N, Forrest ARR:
“Interactive visualization and analysis of large-scale sequencing datasets using ZENBU.” Nature Biotechnology 32(3): 217-219 (2014). PubMed ID 24727769.

 

Biopython
Please cite this paper to refer to Biopython:
Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, De Hoon MJL:
“Biopython: freely available Python tools for computational molecular biology and bioinformatics.” Bioinformatics 25(11): 1422-1423 (2009). PubMed ID 19304878.

 

Open Source Clustering Software
Please cite this paper to refer to Cluster 3.0, Pycluster, or Algorithm::Cluster:
De Hoon MJL, Imoto S, Nolan J, Miyano S.: “Open source clustering software.” Bioinformatics 20(9): 1453-1454 (2004). PubMed ID 14871861.