先看看paralogue（旁係同源的基因）。
同一生物體有兩組基因組，有著共同的來源，但卻有差異。像是人體中 alpha-hemoglobin和beta-hemoglobin，這兩種蛋白質執行相同的功能（血紅蛋白，生物體內負責運載氧的一種蛋白質），但卻屬於不同的基因組，稱為paralogue。
再來看orthologue（直係同源的基因）。
不同生物體不同種間的兩組基因組，但是卻有相同功能，像是人和老鼠有部分的酵素（酶）是相同的，我們稱這兩種蛋白質的基因組為orthologue。othologue is the British spelling。
Homologous genes have shared a common evolutionary ancestor. Note that homology and similarity are not the same thing - genes which are homologous may have high or low similarity, but the presence of similarity doesn't necessarily make two sequences homologues (could be convergent evolution).
Paralogous and orthologous genes are subdivisions of homologous genes. All homologs are either orthologs or paralogs. Orthologs arise because of speciation events.
Thus if a rat and a human sequence have simply diverged since the last common ancestor of rats and humans, then they are orthologs.
Paralogs arise because of gene duplication events. Thus there may be an alpha and beta form of a human protein which have arisen through gene duplication, and then diverged. These two genes are paralogs.
Also note that if this duplication occurred before the last common human-rat ancestor then alpha-human is a paralog to beta-rat, but an ortholog to alpha-rat.
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