Question: Replacement for Tribe-MCL?
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gravatar for Ace
10 weeks ago by
Ace10
Ace10 wrote:

I am looking to find gene families from transcriptome and genome data. Tribe-MCL seems to no longer be available, does anyone know what has replaced it? Sorry if this is a silly question.

ADD COMMENTlink written 10 weeks ago by Ace10

Are you specifically looking for an (exact) replacement of tribe-mcl or would any other protein clustering do as well?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by lieven.sterck2.3k

I would be willing to try any clustering program with a good track record of retrieving gene families which may contain repetitive sequences. Ease of use would be an additional factor I would consider.

ADD REPLYlink written 10 weeks ago by Ace10

You could have a look into for instance orthomcl or orthoFinder (newer) . They should do a fairly similar thing as Tribe-MCL, though not exactly the same as they are more focused on finding "orthologs" (in laymen terms: they tend to cluster more tightly giving smaller/stricter cluster/gene-fams)

btw: There is another Biostars post: A: A Query For The Program Of Tribe-Mcl where the author of tribe-mcl explains how to reproduce the workflow of tribe-mcl

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by lieven.sterck2.3k
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