Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

被引：357

作者：

Wu, Martin ^{[1
]}

Scott, Alexandra J. ^{[1
]}

机构：

[1] Univ Virginia, Dept Biol, Charlottesville, VA 22904 USA

来源：

BIOINFORMATICS | 2012年 / 28卷 / 07期

关键词：

MAXIMUM-LIKELIHOOD; INFERENCE; PLACEMENT;

D O I：

10.1093/bioinformatics/bts079

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 100x faster in metagenomic phylotyping.

引用

页码：1033 / 1034

页数：2

共 12 条

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