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Items: 1 to 20 of 116


PHYRN: a robust method for phylogenetic analysis of highly divergent sequences.

Bhardwaj G, Ko KD, Hong Y, Zhang Z, Ho NL, Chintapalli SV, Kline LA, Gotlin M, Hartranft DN, Patterson ME, Dave F, Smith EJ, Holmes EC, Patterson RL, van Rossum DB.

PLoS One. 2012;7(4):e34261. doi: 10.1371/journal.pone.0034261. Epub 2012 Apr 13.


Phylogenetic profiles reveal evolutionary relationships within the "twilight zone" of sequence similarity.

Chang GS, Hong Y, Ko KD, Bhardwaj G, Holmes EC, Patterson RL, van Rossum DB.

Proc Natl Acad Sci U S A. 2008 Sep 9;105(36):13474-9. doi: 10.1073/pnas.0803860105. Epub 2008 Sep 2.


Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.


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.


Evaluating the relationship between evolutionary divergence and phylogenetic accuracy in AFLP data sets.

García-Pereira MJ, Caballero A, Quesada H.

Mol Biol Evol. 2010 May;27(5):988-1000. doi: 10.1093/molbev/msp315. Epub 2009 Dec 21.


The effect of the guide tree on multiple sequence alignments and subsequent phylogenetic analyses.

Nelesen S, Liu K, Zhao D, Linder CR, Warnow T.

Pac Symp Biocomput. 2008:25-36.


Mind the gaps: evidence of bias in estimates of multiple sequence alignments.

Golubchik T, Wise MJ, Easteal S, Jermiin LS.

Mol Biol Evol. 2007 Nov;24(11):2433-42. Epub 2007 Aug 20.


A hierarchical model for incomplete alignments in phylogenetic inference.

Cheng F, Hartmann S, Gupta M, Ibrahim JG, Vision TJ.

Bioinformatics. 2009 Mar 1;25(5):592-8. doi: 10.1093/bioinformatics/btp015. Epub 2009 Jan 15.


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.


Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences.

Auch AF, Henz SR, Holland BR, Göker M.

BMC Bioinformatics. 2006 Jul 19;7:350.


PICS-Ord: unlimited coding of ambiguous regions by pairwise identity and cost scores ordination.

Lücking R, Hodkinson BP, Stamatakis A, Cartwright RA.

BMC Bioinformatics. 2011 Jan 7;12:10. doi: 10.1186/1471-2105-12-10.


Performance comparison between k-tuple distance and four model-based distances in phylogenetic tree reconstruction.

Yang K, Zhang L.

Nucleic Acids Res. 2008 Mar;36(5):e33. doi: 10.1093/nar/gkn075. Epub 2008 Feb 22.


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.


Scoredist: a simple and robust protein sequence distance estimator.

Sonnhammer EL, Hollich V.

BMC Bioinformatics. 2005 Apr 27;6:108.


Evolutionary distances in the twilight zone--a rational kernel approach.

Schwarz RF, Fletcher W, Förster F, Merget B, Wolf M, Schultz J, Markowetz F.

PLoS One. 2010 Dec 31;5(12):e15788. doi: 10.1371/journal.pone.0015788.


A knowledge-based multiple-sequence alignment algorithm.

Nguyen KD, Pan Y.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):884-96. doi: 10.1109/TCBB.2013.102.


Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies.

Penner O, Grassberger P, Paczuski M.

PLoS One. 2011 Jan 4;6(1):e14373. doi: 10.1371/journal.pone.0014373.

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