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Items: 1 to 20 of 68

1.

Nephele: genotyping via complete composition vectors and MapReduce.

Colosimo ME, Peterson MW, Mardis S, Hirschman L.

Source Code Biol Med. 2011 Aug 18;6:13. doi: 10.1186/1751-0473-6-13.

2.

CloudBurst: highly sensitive read mapping with MapReduce.

Schatz MC.

Bioinformatics. 2009 Jun 1;25(11):1363-9. doi: 10.1093/bioinformatics/btp236. Epub 2009 Apr 8.

3.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
4.

Integrated gene and species phylogenies from unaligned whole genome protein sequences.

Stuart GW, Moffett K, Baker S.

Bioinformatics. 2002 Jan;18(1):100-8.

PMID:
11836217
5.
6.

Exploring the relationship between sequence similarity and accurate phylogenetic trees.

Cantarel BL, Morrison HG, Pearson W.

Mol Biol Evol. 2006 Nov;23(11):2090-100. Epub 2006 Aug 4.

PMID:
16891377
7.

DNACLUST: accurate and efficient clustering of phylogenetic marker genes.

Ghodsi M, Liu B, Pop M.

BMC Bioinformatics. 2011 Jun 30;12:271. doi: 10.1186/1471-2105-12-271.

8.

A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping.

Liu Z, Meng J, Sun X.

Biochem Biophys Res Commun. 2008 Apr 4;368(2):223-30. doi: 10.1016/j.bbrc.2008.01.070. Epub 2008 Jan 28.

PMID:
18230342
9.

Comparison of metagenomic samples using sequence signatures.

Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X.

BMC Genomics. 2012 Dec 27;13:730. doi: 10.1186/1471-2164-13-730.

10.

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

Hartmann S, Vision TJ.

BMC Evol Biol. 2008 Mar 26;8:95. doi: 10.1186/1471-2148-8-95.

11.

Whole genome phylogenies for multiple Drosophila species.

Seetharam A, Stuart GW.

BMC Res Notes. 2012 Dec 4;5:670. doi: 10.1186/1756-0500-5-670.

12.

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree.

Matsen FA, Kodner RB, Armbrust EV.

BMC Bioinformatics. 2010 Oct 30;11:538. doi: 10.1186/1471-2105-11-538.

13.

An improved model for whole genome phylogenetic analysis by Fourier transform.

Yin C, Yau SS.

J Theor Biol. 2015 Oct 7;382:99-110. doi: 10.1016/j.jtbi.2015.06.033. Epub 2015 Jul 4.

PMID:
26151589
14.

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics.

Taylor RC.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S1. doi: 10.1186/1471-2105-11-S12-S1.

15.

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

16.

Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

Nagar A, Hahsler M.

BMC Bioinformatics. 2013;14 Suppl 11:S2. doi: 10.1186/1471-2105-14-S11-S2. Epub 2013 Sep 13.

17.

A quantitative genotype algorithm reflecting H5N1 Avian influenza niches.

Wan XF, Chen G, Luo F, Emch M, Donis R.

Bioinformatics. 2007 Sep 15;23(18):2368-75. Epub 2007 Jul 10.

PMID:
17623701
18.

Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method.

Wu X, Wan XF, Wu G, Xu D, Lin G.

Int J Bioinform Res Appl. 2006;2(3):219-48.

PMID:
18048163
19.

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.

Pandya GA, Holmes MH, Petersen JM, Pradhan S, Karamycheva SA, Wolcott MJ, Molins C, Jones M, Schriefer ME, Fleischmann RD, Peterson SN.

BMC Microbiol. 2009 Oct 7;9:213. doi: 10.1186/1471-2180-9-213.

20.

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