Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.
With the explosive growth of bacterial and archaeal sequence data, large-scale phylogenetic analyses present both opportunities and challenges. Here we describe AMPHORA2, an automated phylogenomic inference tool that can be used for high-throughput, high-quality genome tree reconstruction and metagenomic phylotyping. Compared with its predecessor, AMPHORA2 has several major enhancements and new functions: it has a greatly expanded phylogenetic marker database and can analyze both bacterial and archaeal sequences; it incorporates probability-based sequence alignment masks that improve the phylogenetic accuracy; it can analyze DNA as well as protein sequences and is more sensitive in marker identification; finally, it is over 100× faster in metagenomic phylotyping.
http://wolbachia.biology.virginia.edu/WuLab/Software.html.
Supplementary data are available at Bioinformatics online.
随着细菌和古菌序列数据的爆炸式增长，大规模的系统发育分析既带来了机遇，也带来了挑战。本文介绍了 AMPHORA2，这是一种自动化的基因组系统发育推断工具，可用于高通量、高质量的基因组树重建和宏基因组分群。与前一版本相比，AMPHORA2 有几个主要的增强和新功能：它具有一个大大扩展的系统发育标记数据库，可分析细菌和古菌序列；它包含基于概率的序列比对掩码，可提高系统发育准确性；它可以分析 DNA 和蛋白质序列，并且在标记识别方面更敏感；最后，在宏基因组分群方面，它的速度快了 100 多倍。
http://wolbachia.biology.virginia.edu/WuLab/Software.html。
补充数据可在 Bioinformatics 在线获取。
