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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 100× 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.
Wu et al. (2012) studied this question.