https://bogdan.org.ua/2013/07/09/multiparanoid-vs-quickparanoid-pro-et-contra-for-each.html Tiny bits of bioinformatics, [web-]programming etc Mon, 01 Jan 2024 17:12:20 +0000 hourly 1 https://wordpress.org/?v=3.8.27 https://bogdan.org.ua/2013/07/09/multiparanoid-vs-quickparanoid-pro-et-contra-for-each.html#comment-331539 Thu, 19 Feb 2015 14:31:15 +0000 http://bogdan.org.ua/?p=1931#comment-331539 Matteo, you are right, of course. Multiparanoid output was only better for me in that specific project I was working on. Overall, I liked quickparanoid more.
I had even used quickparanoid in another project. If you are interested, here’s a simple patch to ‘qp’ to allow running quickparanoid non-interactively:
https://bitbucket.org/qmentis/clusterscluster/src/41e4b2d5716f5b1d416b3abaef8b3214b54d9b9a/quickparanoid/qp.patch

]]> https://bogdan.org.ua/2013/07/09/multiparanoid-vs-quickparanoid-pro-et-contra-for-each.html#comment-331533 Thu, 19 Feb 2015 13:38:47 +0000 http://bogdan.org.ua/?p=1931#comment-331533 It is very dangerous to infer that multiparanoid it was best for you since it gives larger clusters. It depends on what you need. If you need orthologs, size of the clusters is not at all a pertinent measure. In principle e.g. the best clustering would minimize the presence of multiple proteins from the same organism and so on

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