Looking For Better Hcluster_Sg Documentation Or Alternative Clustering Methods For The Ensembl Compara Pipeline

Question

[suzanne.mcgaugh]

Hi All,

I'd like to try to use ensembl compara pipeline, but the Hcluster_sg documentation leaves something to be desired. Is there better documentation out there than what is given here? http://treesoft.svn.sourceforge.net/viewvc/treesoft/branches/lh3/hcluster/ Would it be possible to use USEARCH to cluster across transcriptomes and start the ensembl compara pipeline at the MCOFFEE step? Thoughts?

Thanks in advance for any thoughts or info. Sue

Answer 1

[Matthieu - Ensembl Compara]

Hi Suzanne

There is a bit more documentation on the old treefam website: http://legacy.treefam.org/cgi-bin/misc_page.pl?faq#cluster

Regarding the Ensembl Compara pipeline, it is indeed possible to use another clustering algorithm. For instance, we currently also support an HMM-based clustering. Other methods can be implemented, but they're likely to require a bit of coding.

[David Managadze]

Hi Matthieu,

What do you mean in "HMM-based clustering"? Could you please point to the resource where the algorithm is described in details?

Thanks.