I constructed a tree with 30000 different sequences using MAFFT software. After that I applied the cluster algorithm implemented in MCL (http://micans.org/mcl/) and obtained a file with the clustering data.
My question is if you know some software to visualize the output from MCL in a graphica manner. I have tried GAP, but the software is not recognizing the format of the file produced by MCL.
I would appreciate any advice. I am enclosing the result file from MCL.
Francisco,
Cytoscape can handle up to about 1 million edges. If you have more than that, you want to look into using Pythoscape which is built for visualizing large networks. Let me know if you have further questions about these tools.
-Janelle
Dear Fransisco ,
I think this link has capability of answer your questions :
http://www.cgl.ucsf.edu/cytoscape/cluster/clusterMaker.html
best
HAH
Francisco,
Cytoscape can handle up to about 1 million edges. If you have more than that, you want to look into using Pythoscape which is built for visualizing large networks. Let me know if you have further questions about these tools.
-Janelle
I suggest http://www.biolayout.org/ the same author from http://micans.org/mcl/ was involved. And I am sure it will handle very large network. For MCL format support see last paragraph in this link http://www.biolayout.org/support/faq/ . Here http://www.biolayout.org/support/requirements/ they say "The current limit for rendering large networks with a 64bit 8Gb machine is somewhere around 45,000 nodes & 5 million edges, at least in our hands."
Here is a good software for clustering homologous sequences, it can handle enormous amount of data (from command line) ...
http://bioinfoserver.rsbs.anu.edu.au/programs/clans/
Thanks everyone for your answers... Looks that I have a lot of work to do... I will keep you updated folks !...
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