Pajek

• Documentation:  http://mrvar.fdv.uni-lj.si/pajek/pajekman.pdf

• (Mrvar, 2016) Analysis and visualization of large networks with program package Pajek. Complex Adaptive Systems Modeling. Complex Adaptative S.
  DOI: 10.1186/s40294-016-0017-8
• (Batagelj, 2014) Pajek. Encyclopedia of Social Network Analysis and Mining. ESNAM.
  DOI: 10.1007/978-1-4614-6170-8_310
• (Batagelj, 2002) Pajek— Analysis and Visualization of Large Networks. Graph Drawing.
  DOI: 10.1007/3-540-45848-4_54

Faculty of Social Sciences, University of Ljubljana, Ljubljana, Slovenia; Institute of Mathematics, Physics and Mechanics, University of Ljubljana, Ljubljana, Slovenia

Benchmarking

• (Agapito et al., 2013)  Visualization of protein interaction networks: problems and solutions. BMC bioinformatics.
  PMID:  23368786
• (Kramer et al., 2014)  R-based software for the integration of pathway data into bioinformatic algorithms. Biology.
  PMID:  24833336
• (Suderman and Hallett, 2007)  Tools for visually exploring biological networks. Bioinformatics.
  PMID:  17720984
• (Gehlenborg et al., 2010)  Visualization of omics data for systems biology. Nature methods.
  PMID:  20195258
• (Pavlopoulos et al., 2008)  A survey of visualization tools for biological network analysis. BioData mining.
  PMID:  19040716
• (O'Donoghue et al., 2010)  Visualizing biological data-now and in the future. Nature methods.
  PMID:  20195254