title: Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://wolbachia.biology.virginia.edu/WuLab/Software.html.
  
  
  BACKGROUND
  mw4yv@virginia.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, University of Virginia, Charlottesville, VA 22904, USA. mw4yv@virginia.edu
authors.forename: Martin
authors.initials: M
authors.lastname: Wu
authors.forename: Alexandra J
authors.initials: AJ
authors.lastname: Scott
mesh_terms: D000465:Algorithms; D001105:Archaea / Q000145:classification / Q000235:genetics*; D001419:Bacteria / Q000145:classification / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D054892:Metagenome; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods; D012984:Software