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1. AMPHORA
   • Download here http://bobcat.genomecenter.ucdavis.edu/AMPHORA
   • Described in "Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol 2008 Oct 13; 9(10) R151. doi:10.1186/gb-2008-9-10-r151 " and available here http://genomebiology.com/2008/9/10/R151#B41
2. STAP
   • Download here http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/STAP_download
   • Described in Wu D, Hartman A, Ward N, and Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS ONE 2008 Jul 2; 3(7) e2566. doi:10.1371/journal.pone.0002566 and available here http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002566

Publications

1. pmid= 9909313

2. Wu M and Eisen JA. A simple, fast, and accurate method of phylogenomic inference. Genome Biol. 2008 Oct 13;9(10):R151. DOI:10.1186/gb-2008-9-10-r151 |
3. Wu D, Hartman A, Ward N, and Eisen JA. An automated phylogenetic tree-based small subunit rRNA taxonomy and alignment pipeline (STAP). PLoS One. 2008 Jul 2;3(7):e2566. DOI:10.1371/journal.pone.0002566 |

News

Check out the blog of Jonathan Eisen