基因加倍：tandem duplication和segmental duplication的区别与联系：

Gene duplications are considered to be one of the primary driving forces in the evolution of genomes and genetic systems [22]. Duplicated genes provide raw material for the generation of new genes, which, in turn, facilitate the generation of new functions. Segmental duplication, tandem duplication, and transposition events, such as retroposition and replicative transposition [23], are considered to represent three principal evolutionary patterns. Of these patterns, segmental and tandem duplications have been suggested to represent two of the main causes of gene family expansion in plants [24]. Segmental duplications multiple genes through polyploidy followed by chromosome rearrangements [25]. It occurs most frequently in plants because most plants are diploidized polyploids and retain numerous duplicated chromosomal blocks within their genomes [24]. Tandem duplications were characterized as multiple members of one family occurring within the same intergenic region or in neighboring intergenic regions [26]. In this study, we defined tandem duplicated genes as adjacent homologous genes on a single chromosome, with no more than one intervening gene. For this analysis, we focused on segmental and tandem duplication events. To gain a greater insight about the expansion pattern of soybean expansin genes in this huge gene family, we identified tandem duplicated clusters based on the gene locus, and searched the Plant Genome Duplication Database [27] to locate segmentally duplicated pairs.

参考文献：

以上是基因加倍和串联重复定义，可以用blast方法。在我们课程当中是根据基因之间的同源比对来分析的；参考文献如下：

https://link.springer.com/article/10.1007/s00425-016-2575-6

第二种方法：也就是采用MCscanX的方法找大片段的重复和串联重复基因，也可以分析，结果如下，课程已经更新这一节内容《基因家族分析实操课程》：

更多生物信息课程：

1. 文章越来越难发？是你没发现新思路，基因家族分析发2-4分文章简单快速，学习链接：基因家族分析实操课程、基因家族文献思路解读

2. 转录组数据理解不深入？图表看不懂？点击链接学习深入解读数据结果文件，学习链接：转录组（有参）结果解读；转录组（无参）结果解读

3. 转录组数据深入挖掘技能-WGCNA，提升你的文章档次，学习链接：WGCNA-加权基因共表达网络分析

4. 转录组数据怎么挖掘？学习链接：转录组标准分析后的数据挖掘、转录组文献解读

5. 微生物16S/ITS/18S分析原理及结果解读、OTU网络图绘制、cytoscape与网络图绘制课程

6. 生物信息入门到精通必修基础课：linux系统使用、perl入门到精通、perl语言高级、R语言画图

7. 医学相关数据挖掘课程，不用做实验也能发文章：TCGA-差异基因分析、GEO芯片数据挖掘、 GEO芯片数据不同平台标准化 、GSEA富集分析课程、TCGA临床数据生存分析、TCGA-转录因子分析、TCGA-ceRNA调控网络分析

8.其他，二代测序转录组数据自主分析、NCBI数据上传、二代测序数据解读、