TribeMCL is a method for clustering proteins into related groups, which are termed 'protein families'. TribeMCL uses a novel clustering method (Markov Clustering or MCL) which solves problems which normally hinder protein sequence clustering. These problems include: multi-domain proteins, peptide fragments and proteins which possess domains which are very widespread (promiscuous domains).

More on clustering using MCL algorithm

Reference: Enright A.J., Van Dongen S., Ouzounis C.A; Nucleic Acids Res. 30(7):1575-1584 (2002) [PDF]

Gene names and Tribe names:
The nomenclature of chloroplast genes has gone through considerable revision in the years since the first chloroplast genomes were sequenced (Stoebe et al, 1998). The accelerated pace of chloroplast genome sequencing in recent years assures that new chloroplast genes will continue to be discovered and nomenclature will need to reflect those discoveries. Chloroplast DB does not override annotated gene names, and so orthologous annotated genes may have different names in Chloroplast DB. An example is cysA. As of September 1, 2005, this gene is annotated as cysA in four genomes, mbpX in one genome, and ycf85 in two other genomes. The Tribe function of chloroplast DB can help identify potentially orthologous genes that have been assigned different names by different investigators. A simple rule was used to assign valid chloroplast gene names to Tribes based on the names of valid chloroplast genes found in that tribe. Valid names were determined from the current version of Uniprot Database's "List of chloroplast and cyanelle encoded proteins." If Tribes contained exactly one valid name, that name was assigned to the tribe. If a tribe contained more than one Uniprot name, then all valid names were assigned seperated by a '/'. In two cases (ccsA and ycf32), the name was both a Uniprot name and a synonym for another Uniprot name (chlI and psbY, respectively). If it tribe contains only genes that have an ambiguous name, or no Uniprot name at all, it is marked by 'ambig[ | ]'. If other genes in the tribe are unambiguously named, the tribe will be named with that gene. If a tribe included no gene with a valid Uniprot name, the tribe was left unnamed. Multiple tribes may have a particular name, and multiple valid names may be found in a tribe. The tribe number and the genes that are contained within them are always unique.

References

Uniprot list chloroplast and cyanelle proteins: 47.6, 2 August 2005

Stoebe B., Martin W., Kowallik K.V.
Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes.
Plant Mol. Biol. Report. 16:243(1998).