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Analyzing patterns of microbial evolution using the mauve genome alignment system.
Darling AE, Treangen TJ, Messeguer X, Perna NT. Darling AE, et al. Methods Mol Biol. 2007;396:135-52. doi: 10.1007/978-1-59745-515-2_10. Methods Mol Biol. 2007. PMID: 18025691
The impact of the neisserial DNA uptake sequences on genome evolution and stability.
Treangen TJ, Ambur OH, Tonjum T, Rocha EP. Treangen TJ, et al. Genome Biol. 2008;9(3):R60. doi: 10.1186/gb-2008-9-3-r60. Epub 2008 Mar 26. Genome Biol. 2008. PMID: 18366792 Free PMC article.
A novel heuristic for local multiple alignment of interspersed DNA repeats.
Treangen TJ, Darling AE, Achaz G, Ragan MA, Messeguer X, Rocha EP. Treangen TJ, et al. IEEE/ACM Trans Comput Biol Bioinform. 2009 Apr-Jun;6(2):180-9. doi: 10.1109/TCBB.2009.9. IEEE/ACM Trans Comput Biol Bioinform. 2009. PMID: 19407343
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.
Enk J, Devault A, Debruyne R, King CE, Treangen T, O'Rourke D, Salzberg SL, Fisher D, MacPhee R, Poinar H. Enk J, et al. Genome Biol. 2011;12(5):R51. doi: 10.1186/gb-2011-12-5-r51. Epub 2011 May 31. Genome Biol. 2011. PMID: 21627792 Free PMC article.
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, Koren S, Treangen TJ, Schatz MC, Delcher AL, Roberts M, Marçais G, Pop M, Yorke JA. Salzberg SL, et al. Genome Res. 2012 Mar;22(3):557-67. doi: 10.1101/gr.131383.111. Epub 2012 Jan 6. Genome Res. 2012. PMID: 22147368 Free PMC article.
MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M. Treangen TJ, et al. Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2. Genome Biol. 2013. PMID: 23320958 Free PMC article.
MetAMOS can be downloaded from:
MetAMOS can be downloaded from:
Automated ensemble assembly and validation of microbial genomes.
Koren S, Treangen TJ, Hill CM, Pop M, Phillippy AM. Koren S, et al. BMC Bioinformatics. 2014 May 3;15:126. doi: 10.1186/1471-2105-15-126. BMC Bioinformatics. 2014. PMID: 24884846 Free PMC article.
Mash: fast genome and metagenome distance estimation using MinHash.
Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH, Koren S, Phillippy AM. Ondov BD, et al. Among authors: treangen tj. Genome Biol. 2016 Jun 20;17(1):132. doi: 10.1186/s13059-016-0997-x. Genome Biol. 2016. PMID: 27323842 Free PMC article.
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