Summary: 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 ×ばつ faster in metagenomic phylotyping.

Availability: http://wolbachia.biology.virginia.edu/WuLab/Software.html.

Contact: mw4yv@virginia.edu

Supplementary information: Supplementary data are available at Bioinformatics online.