Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.


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.



Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Algorithms
  • Archaea / classification
  • Archaea / genetics*
  • Bacteria / classification
  • Bacteria / genetics*
  • Computational Biology / methods*
  • Genome, Archaeal
  • Genome, Bacterial
  • Genomics / methods*
  • Metagenome
  • Phylogeny*
  • Sequence Alignment
  • Sequence Analysis, DNA / methods
  • Sequence Analysis, Protein / methods
  • Software