虽然曾经在Blog上贴过NCBI关于这两个词的解释的示意图，不过今天觉得对这两个重要的名词还是有必要好好说一说：
原图见http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Orthology.html
且看文字说明：
Homologous sequences. Orthologs and Paralogs are two types of homologous sequences. Orthology describes genes in different species that derive from a common ancestor. Orthologous genes may or may not have the same function. Paralogy describes homologous genes within a single species that diverged by gene duplication.
简单翻译一下：
Orthologs 和 Paralogs 是同源序列的两种类型。
Orthology描述在不同物种中来自于共同祖先的基因。Orthologous基因可能有相同的功能，也可能没有。Paralogy描述在同一物种内由于基因复制而分离的同源基因。
Orthology通常译作直系同源、直向同源、垂直同源。Paralogy通常译作旁系同源、并系同源、横向同源。
然而，NCBI的Glossary中对paralog的定义是： A paralog is one of a set of homologous genes that have diverged from each other as a consequence of gene duplication. For example, the mouse a-globin and b-globin genes are paralogs. The relationship between mouse a-globin and chick b-globin is also considered paralogous (see the figure).
即，祖先基因经过复制后分离产生的基因是paralog，例如鼠的a球蛋白和b球蛋白基因。并且，鼠的a球蛋白和鸡的b球蛋白基因的关系也是paralog。
因此不能说：来自不同物种的就不是paralog。这一点就与前面的定义不一致了，前面说：“Paralogy describes homologous genes within a single species that diverged by gene duplication.”
对ortholog的定义是： Orthology describes genes in different species that derive from a single ancestral gene in the last common ancestor of the respective species.
即，Orthology 指的是这样一些基因，它们起源于这些基因所在物种的最近的共同祖先的一条基因。（有点拗口，但也想不出更好的译法了）
TRENDS in Genetics Vol.18 No.12 December 2002 的一篇文章：《Orthology, paralogy and proposed classification for paralog subtypes》对两者的定义做了进一步的探究。作者指出：Paralogs are defined as genes that derive from a single gene that was duplicated within a genome.The latter definition does not specify that paralogs can only be found in a single organism, and hence genes in different organisms that arose from gene duplication in an ancestral genome are also paralogs according to the definition。
作者根据复制事件与物种分化事件发生的先后关系，提出了inparalog和outparalog的概念，对于一个给定的世系，在物种分化后发生复制事件产生的基因称为inparalog，而复制事件在分化之前，则称为outparalog。具体的例子我就不说了，有兴趣可以看看原文。