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FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP. Price MN, et al. PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490. PLoS One. 2010. PMID: 20224823 Free PMC article.
The MicrobesOnline Web site for comparative genomics.
Alm EJ, Huang KH, Price MN, Koche RP, Keller K, Dubchak IL, Arkin AP. Alm EJ, et al. Genome Res. 2005 Jul;15(7):1015-22. doi: 10.1101/gr.3844805. Genome Res. 2005. PMID: 15998914 Free PMC article.
Model discrimination using data collaboration.
Feeley R, Frenklach M, Onsum M, Russi T, Arkin A, Packard A. Feeley R, et al. J Phys Chem A. 2006 Jun 1;110(21):6803-13. doi: 10.1021/jp056309s. J Phys Chem A. 2006. PMID: 16722696
Memory in microbes: quantifying history-dependent behavior in a bacterium.
Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, Arkin AP. Wolf DM, et al. PLoS One. 2008 Feb 27;3(2):e1700. doi: 10.1371/journal.pone.0001700. PLoS One. 2008. PMID: 18324309 Free PMC article.
FastBLAST: homology relationships for millions of proteins.
Price MN, Dehal PS, Arkin AP. Price MN, et al. PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31. PLoS One. 2008. PMID: 18974889 Free PMC article.
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