Phylogenomic Analysis of Bacterial and Archaeal Sequences with AMPHORA2.

  • Wu M
  • Scott A
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Abstract

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 to 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. AVAILABILITY: http://wolbachia.biology.virginia.edu/WuLab/Software.html. CONTACT: mw4yv@virginia.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Authors

  • Martin Wu

  • Alexandra J Scott

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