直系同源(orthologous) 指的是不同物种之间的同源性，例如蛋白质的同源性，DNA序列的同源性。

Orthologs是指来自于不同物种的由垂直家系（物种形成）进化而来的蛋白，并且典型的保留与原始蛋白有相同的功能。

旁系同源（Paralogs）是那些在一定物种中的来源于基因复制的蛋白，可能会进化出新的与原来有关的功能。

蛋白质同源家庭的分析对于确立物种之间的亲缘关系和预测新蛋白质序列的功能有重要意义，同源蛋白质（homolog）进一步划分为直系同源（ortholog）和旁系同源（paralog），前者指不同物种中具有相同功能和共同起源的基因，后者则指在同一物种内具有不同功能，但也有共同起源的基因，例如同是起源于珠蛋白的α珠蛋白、β珠蛋白和肌红蛋白。

paralog、ortholog释义

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/Orthology.html

http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/orthologs3.gif

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。
 As we know ,there are two kinds of homolog, ortholog and paralog. Genes in two  species that have directly evolved from a single gene in the last common ancestor are called orthologs. A set of homologous genes that have diverged from each other as a consequence of genetic duplication are called paralogs. Sometime
those paralogs which arose from a duplication after the speciation event are called in-paralogs.