Best bioinformatics software for venn diagram
Venn diagrams are very simple, yet incredibly useful tools used to show all logical relations between finite collections of different sets of data. In Venn diagrams, sets of data are often represented as overlapping circles. Data that are shared between two different sets will reside at the intersection, while unique data remain outside the intersection.
Venn diagrams in biology
In biology and omics, Venn diagrams can be used for a variety of purposes, such as the comparison of different lists of genes or proteins (generally 2 or 3) to identify similarities and represent them in two dimensions. Most softwares allow easy extraction of the data, and let you customize the diagrams.
Continuing our series of data visualization tools, OMICtools members voted for their favorite Venn diagram representation softwares and websites. Here are the results from 54 voters.
First position for Venny
You were 50% to choose Venny as your number 1 favorite tool to generate Venn diagrams.
Venny is a webserver created by Juan Carlos Oliveros from the BioinfoGP service at the Spanish National Biotechnology Centre, that can be used online or offline to generate Venn diagrams from up to four lists. Its straightforward usage lets you create diagrams and extract data in 3 basic steps:

Paste your lists of data (one element per row) and rename the lists

Click on the numbers to get exclusive and common data between lists

Rightclick the figure to view and save the diagram
Venny allows basic customization of your diagrams (line weight, font size and style).
Second position for BioVenn and Venn diagram
43% of the OMICtools community voted for Biovenn and Venn diagram as their favorite tool!
BioVenn
BioVenn is a web application developed at the Centre for Molecular and Biomolecular Informatics that enables creation of Venn diagrams from up to 3 sets of data. Unlike in Venny, the diagrams in BioVenn are areaproportional, which means that the size of the circles and the overlaps correspond to the sizes of the data sets. BioVenn also comes with interesting features, such as the ability to directly upload a data set from a tab file, or to support a wide range of identifiers which can be linked to biological databases.
Venn diagram
Venn diagram was developed by the VIBUgen Center for Plant Systems Biology at Ghent University. This web application allows users to draw Venn diagrams from up to 6 data lists, in a symmetric or nonsymmetric fashion. The diagrams can then be downloaded in SVG or PNG format. Moreover, Venn diagram is able to calculate the intersections of up to 30 different lists, making it a useful tool to identify common values between multiple data sets.
Third position for InteractiVenn
A very close third place goes to InteractiVenn, chosen by 41% of voters as their favorite tool. InteractiVenn is a sophisticated and flexible webbased tool that allows creation of Venn diagrams from up to 6 lists and analysis of set unions, while preserving the shape of the diagram. By displaying partial unions, the user is able to locate regions that combine unions of sets and their intersections, thus providing additional observations on the interactions between joined sets.
With InteractiVenn, the user can choose text size, color, opacity, and can export the diagram in a vectored format. Datasets can also be saved locally for later use on the website.
References
(Oliveros, J.C., 20072015) Venny. An interactive tool for comparing lists with Venn’s diagrams. http://bioinfogp.cnb.csic.es/tools/venny/index.html
(Hulsen et al., 2008) BioVenn – a web application for the comparison and visualization of biological lists using areaproportional Venn diagrams. BMC Genomics.
Venn diagram: http://bioinformatics.psb.ugent.be/webtools/Venn/
(Heberle et al., 2015) InteractiVenn: a webbased tool for the analysis of sets through Venn diagrams. BMC Bioinformatics.