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Results: 1 to 20 of 97

1.

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.

Magori-Cohen R, Louzoun Y, Kleinstein SH.

Bioinformatics. 2006 Jul 15;22(14):e332-40.

PMID:
16873490
[PubMed - indexed for MEDLINE]
Free Article
2.

Efficient inference on known phylogenetic trees using Poisson regression.

Rosset S.

Bioinformatics. 2007 Jan 15;23(2):e142-7.

PMID:
17237083
[PubMed - indexed for MEDLINE]
Free Article
3.

ProfDist: a tool for the construction of large phylogenetic trees based on profile distances.

Friedrich J, Dandekar T, Wolf M, Müller T.

Bioinformatics. 2005 May 1;21(9):2108-9. Epub 2005 Jan 27.

PMID:
15677706
[PubMed - indexed for MEDLINE]
Free Article
4.

Using evolutionary Expectation Maximization to estimate indel rates.

Holmes I.

Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24.

PMID:
15731213
[PubMed - indexed for MEDLINE]
Free Article
5.

Linkage disequilibrium for different scales and applications.

Mueller JC.

Brief Bioinform. 2004 Dec;5(4):355-64. Review.

PMID:
15606972
[PubMed - indexed for MEDLINE]
Free Article
6.

Representation in stochastic search for phylogenetic tree reconstruction.

Weber G, Ohno-Machado L, Shieber S.

J Biomed Inform. 2006 Feb;39(1):43-50. Epub 2005 Nov 28.

PMID:
16359929
[PubMed - indexed for MEDLINE]
Free Article
7.

Computing the all-pairs quartet distance on a set of evolutionary trees.

Stissing M, Mailund T, Pedersen CN, Brodal GS, Fagerberg R.

J Bioinform Comput Biol. 2008 Feb;6(1):37-50.

PMID:
18324744
[PubMed - indexed for MEDLINE]
8.

Fast NJ-like algorithms to deal with incomplete distance matrices.

Criscuolo A, Gascuel O.

BMC Bioinformatics. 2008 Mar 26;9:166. doi: 10.1186/1471-2105-9-166.

PMID:
18366787
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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
[PubMed - indexed for MEDLINE]
Free Article
10.
11.

Phylogenetic trees based on gene content.

Huson DH, Steel M.

Bioinformatics. 2004 Sep 1;20(13):2044-9. Epub 2004 Mar 25.

PMID:
15044248
[PubMed - indexed for MEDLINE]
Free Article
12.

Phylocomposer and phylodirector: analysis and visualization of transducer indel models.

Holmes I.

Bioinformatics. 2007 Dec 1;23(23):3263-4. Epub 2007 Sep 5.

PMID:
17804439
[PubMed - indexed for MEDLINE]
Free Article
13.

DPRml: distributed phylogeny reconstruction by maximum likelihood.

Keane TM, Naughton TJ, Travers SA, McInerney JO, McCormack GP.

Bioinformatics. 2005 Apr 1;21(7):969-74. Epub 2004 Oct 28.

PMID:
15513992
[PubMed - indexed for MEDLINE]
Free Article
14.

Upper bounds on maximum likelihood for phylogenetic trees.

Hendy MD, Holland BR.

Bioinformatics. 2003 Oct;19 Suppl 2:ii66-72.

PMID:
14534174
[PubMed - indexed for MEDLINE]
Free Article
15.

Estimating hypermutation rates from clonal tree data.

Kleinstein SH, Louzoun Y, Shlomchik MJ.

J Immunol. 2003 Nov 1;171(9):4639-49.

PMID:
14568938
[PubMed - indexed for MEDLINE]
Free Article
16.

Tree and rate estimation by local evaluation of heterochronous nucleotide data.

Yang Z, O'Brien JD, Zheng X, Zhu HQ, She ZS.

Bioinformatics. 2007 Jan 15;23(2):169-76. Epub 2006 Nov 16.

PMID:
17110369
[PubMed - indexed for MEDLINE]
Free Article
17.

Robust inference of positive selection from recombining coding sequences.

Scheffler K, Martin DP, Seoighe C.

Bioinformatics. 2006 Oct 15;22(20):2493-9. Epub 2006 Aug 7.

PMID:
16895925
[PubMed - indexed for MEDLINE]
Free Article
18.

The distribution of distances between randomly constructed genomes: generating function, expectation, variance and limits.

Xu W.

J Bioinform Comput Biol. 2008 Feb;6(1):23-36.

PMID:
18324743
[PubMed - indexed for MEDLINE]
19.

Evolutionary simulations to detect functional lineage-specific genes.

Dupanloup I, Kaessmann H.

Bioinformatics. 2006 Aug 1;22(15):1815-22. Epub 2006 Jun 9.

PMID:
16766551
[PubMed - indexed for MEDLINE]
Free Article
20.

Integrating B cell lineage information into statistical tests for detecting selection in Ig sequences.

Uduman M, Shlomchik MJ, Vigneault F, Church GM, Kleinstein SH.

J Immunol. 2014 Feb 1;192(3):867-74. doi: 10.4049/jimmunol.1301551. Epub 2013 Dec 27.

PMID:
24376267
[PubMed - indexed for MEDLINE]

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