Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes
Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes
复制标题
DOI：
10.1093/bioinformatics/btw583
复制
发表时间：
2017-01-01
期刊：
影响因子：
5.8
通讯作者：
Kellogg, Elizabeth A.
中科院分区：
文献类型：
--
作者：
McKain, Michael R.;Hartsock, Ryan H.;Kellogg, Elizabeth A.
动机：叶绿体基因组现在在数百种用于血管系统发育项目的项目中生产，但是当前的注释，对齐和树木估计的方法仍然需要一些手动干预减少吞吐量，并增加大型叶绿体系统的分析时间。构建的软件套件和数据库是为了利用新颖的注释程序Annobtd。使用Annobtd，Verdant提供了无需手动干预的叶绿体基因组的准确注释。随后的对齐和树木估计可以包含新的注释和公开可用的质体，并且可以容纳大量分类单元。 Verdant急剧减少了分析组装叶绿体基因组所需的时间，并消除了对个人硬件的管道和软件的需求。
Motivation: Chloroplast genomes are now produced in the hundreds for angiosperm phylogenetics projects, but current methods for annotation, alignment and tree estimation still require some manual intervention reducing throughput and increasing analysis time for large chloroplast systematics projects.Results: Verdant is a web-based software suite and database built to take advantage a novel annotation program, annoBTD. Using annoBTD, Verdant provides accurate annotation of chloroplast genomes without manual intervention. Subsequent alignment and tree estimation can incorporate newly annotated and publically available plastomes and can accommodate a large number of taxa. Verdant sharply reduces the time required for analysis of assembled chloroplast genomes and removes the need for pipelines and software on personal hardware.