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Results: 1 to 20 of 107

1.

Phylogenetic assessment of alignments reveals neglected tree signal in gaps.

Dessimoz C, Gil M.

Genome Biol. 2010;11(4):R37. doi: 10.1186/gb-2010-11-4-r37. Epub 2010 Apr 6.

PMID:
20370897
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees.

Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR.

Syst Biol. 2012 Jan;61(1):90-106. doi: 10.1093/sysbio/syr095. Epub 2011 Dec 1.

PMID:
22139466
[PubMed - indexed for MEDLINE]
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
[PubMed - indexed for MEDLINE]
Free Article
4.

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.

PMID:
18366758
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Phylogenetic inference under varying proportions of indel-induced alignment gaps.

Dwivedi B, Gadagkar SR.

BMC Evol Biol. 2009 Aug 23;9:211. doi: 10.1186/1471-2148-9-211.

PMID:
19698168
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments.

Talavera G, Castresana J.

Syst Biol. 2007 Aug;56(4):564-77.

PMID:
17654362
[PubMed - indexed for MEDLINE]
7.

The tree alignment problem.

Varón A, Wheeler WC.

BMC Bioinformatics. 2012 Nov 9;13:293. doi: 10.1186/1471-2105-13-293.

PMID:
23140486
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
11734060
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Ancestral sequence alignment under optimal conditions.

Hudek AK, Brown DG.

BMC Bioinformatics. 2005 Nov 17;6:273.

PMID:
16293191
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Multiple sequence alignment: in pursuit of homologous DNA positions.

Kumar S, Filipski A.

Genome Res. 2007 Feb;17(2):127-35. Review.

PMID:
17272647
[PubMed - indexed for MEDLINE]
Free Article
11.

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.

PMID:
21034504
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support.

Simmons MP, Müller KF, Norton AP.

Mol Phylogenet Evol. 2010 Dec;57(3):1004-16. doi: 10.1016/j.ympev.2010.09.004. Epub 2010 Sep 16.

PMID:
20849963
[PubMed - indexed for MEDLINE]
13.

Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa.

Morrison DA, Ellis JT.

Mol Biol Evol. 1997 Apr;14(4):428-41.

PMID:
9100373
[PubMed - indexed for MEDLINE]
Free Article
14.

Accounting for alignment uncertainty in phylogenomics.

Wu M, Chatterji S, Eisen JA.

PLoS One. 2012;7(1):e30288. doi: 10.1371/journal.pone.0030288. Epub 2012 Jan 17.

PMID:
22272325
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Multiple sequence alignment accuracy and phylogenetic inference.

Ogden TH, Rosenberg MS.

Syst Biol. 2006 Apr;55(2):314-28.

PMID:
16611602
[PubMed - indexed for MEDLINE]
16.

Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees.

Liu K, Raghavan S, Nelesen S, Linder CR, Warnow T.

Science. 2009 Jun 19;324(5934):1561-4. doi: 10.1126/science.1171243.

PMID:
19541996
[PubMed - indexed for MEDLINE]
Free Article
17.

Re-mind the gap! Insertion - deletion data reveal neglected phylogenetic potential of the nuclear ribosomal internal transcribed spacer (ITS) of fungi.

Nagy LG, Kocsubé S, Csanádi Z, Kovács GM, Petkovits T, Vágvölgyi C, Papp T.

PLoS One. 2012;7(11):e49794. doi: 10.1371/journal.pone.0049794. Epub 2012 Nov 19.

PMID:
23185439
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.

Bastien O, Ortet P, Roy S, Maréchal E.

BMC Bioinformatics. 2005 Mar 10;6:49.

PMID:
15757521
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
18229674
[PubMed - indexed for MEDLINE]
Free Article
20.

The impact of rRNA secondary structure consideration in alignment and tree reconstruction: simulated data and a case study on the phylogeny of hexapods.

Letsch HO, Kück P, Stocsits RR, Misof B.

Mol Biol Evol. 2010 Nov;27(11):2507-21. doi: 10.1093/molbev/msq140. Epub 2010 Jun 7.

PMID:
20530152
[PubMed - indexed for MEDLINE]
Free Article

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