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FastTree 2--approximately maximum-likelihood trees for large alignments.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. PLoS One. 2010 Mar 10;5(3):e9490. doi: 10.1371/journal.pone.0009490. PLoS One. 2010. PMID: 20224823 Free PMC article.
MetaMicrobesOnline: phylogenomic analysis of microbial communities.
Chivian D, Dehal PS, Keller K, Arkin AP. Chivian D, et al. Among authors: dehal ps. Nucleic Acids Res. 2013 Jan;41(Database issue):D648-54. doi: 10.1093/nar/gks1202. Epub 2012 Nov 30. Nucleic Acids Res. 2013. PMID: 23203984 Free PMC article.
MicrobesOnline: an integrated portal for comparative and functional genomics.
Dehal PS, Joachimiak MP, Price MN, Bates JT, Baumohl JK, Chivian D, Friedland GD, Huang KH, Keller K, Novichkov PS, Dubchak IL, Alm EJ, Arkin AP. Dehal PS, et al. Nucleic Acids Res. 2010 Jan;38(Database issue):D396-400. doi: 10.1093/nar/gkp919. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906701 Free PMC article.
FastTree: computing large minimum evolution trees with profiles instead of a distance matrix.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. Mol Biol Evol. 2009 Jul;26(7):1641-50. doi: 10.1093/molbev/msp077. Epub 2009 Apr 17. Mol Biol Evol. 2009. PMID: 19377059 Free PMC article.
FastBLAST: homology relationships for millions of proteins.
Price MN, Dehal PS, Arkin AP. Price MN, et al. Among authors: dehal ps. PLoS One. 2008;3(10):e3589. doi: 10.1371/journal.pone.0003589. Epub 2008 Oct 31. PLoS One. 2008. PMID: 18974889 Free PMC article.
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA. Novichkov PS, et al. Among authors: dehal ps. Nucleic Acids Res. 2012 Jul;40(Web Server issue):W604-8. doi: 10.1093/nar/gks562. Epub 2012 Jun 14. Nucleic Acids Res. 2012. PMID: 22700702 Free PMC article.
Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough.
Mukhopadhyay A, Redding AM, Joachimiak MP, Arkin AP, Borglin SE, Dehal PS, Chakraborty R, Geller JT, Hazen TC, He Q, Joyner DC, Martin VJ, Wall JD, Yang ZK, Zhou J, Keasling JD. Mukhopadhyay A, et al. J Bacteriol. 2007 Aug;189(16):5996-6010. doi: 10.1128/JB.00368-07. Epub 2007 Jun 1. J Bacteriol. 2007. PMID: 17545284 Free PMC article.
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