Does anyone know some way to convert the information stored in .shared file in a table, which could be opened by Cytoscape software? Cytoscape allows the visual integration of the network with expression profiles, phenotypes, and other molecular state information. This software could be specially useful creating visual networks screening shared OTUÂ´s between different samples.
I am also very interested in Luis’ post - has anyone experience of this or is the Mothur team going to address this?
Cytoscape needs edges (with a value attached) and nodes, I don’t think you could just ‘convert’ the shared file to another table.
In theory you could export your shared file from mothur using make.biom and run it in Qiime’s make_otu_network.py script. In practice, as I just found out trying that, Qiime is annoying to install, and in the end the make_otu_network.py script exits with a cryptic error message and no output. Maybe you have more luck.