Hello,
I am completely new to Cytoscape, and don't really know how to do what I want, or if Cytoscape does what I'm hoping it does. I have carried out an all-vs-all blastp analysis for 7 eukaryotic species - this was used subsequently for an OrthoMCL analysis of protein groups in these species. What I'm hoping to do is use the blastp output (or even better, the final OrthoMCL groups) and generate network diagrams that depict gene family expansion and/or reduction. I am running this on my Macbook (10.11.2) with 16 GB of RAM.
I noticed a package for Cytoscape called BLAST2SimilarityGraph, but I didn't realize that the package doesn't work with the version of Cytoscape that I've downloaded (3.3). So I'm wondering a couple of things: 1) Do I have to download the old version of Cytoscape and install BLAST2SimilarityGraph? and 2) How might I go about doing this analysis with Cytoscape 3.3, if it is possible? Are there other packages to download that might help?
Thanks in advance!
Ryan