<p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p> <p>Pertinent evolutionary studies are based on a correct use of homology terms such as paralogues, metalogues and orthologues. Such crucial concepts have been applied to
intragenomic and intergenomic analyses. A further requisite is a proper definition of
what is a structural segment of homology. Such segments are called modules to reflect
that they play a role in the mechanism of combinational construction of a gene from
ready-made basic components. Since identifying a module is operationally equivalent
to determining the ancestor to this gene segment, it becomes possible to track back
protein history and genome evolution. Such studies underline the importance of two
fundamental processes, gene duplication and gene fusion. Moreover, grouping the
closest orthologues in families is a pertinent way to reconstruct a genomic tree for all
available prokaryotes.</p>
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Comp Funct Genomics. 2002 Dec; 3(6):488-493