Replacement for Tribe-MCL?

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6.5 years ago

Ace ▴ 90

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.

RNA-Seq Gene Families TribeMCL MCL • 2.9k views

ADD COMMENT • link 6.5 years ago by Ace ▴ 90

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

ADD REPLY • link 6.5 years ago by lieven.sterck 15k

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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 REPLY • link 6.5 years ago by Ace ▴ 90

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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 REPLY • link 6.4 years ago by lieven.sterck 15k

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