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.
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.
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
Hi, We are planning to analyze some cancer cell lines for variants such as mutations, gene fusions and structural variants. I am looking for sequencing …
<p>The chip-seq analysis suite often discussed here, HOMER, seems no longer to be available on line. Does anyone know an alternative source of the documentation/manual? …
Are you specifically looking for an (exact) replacement of tribe-mcl or would any other protein clustering do as well?
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.
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