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Items: 1 to 20 of 547

1.

The tree alignment problem.

Varón A, Wheeler WC.

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

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
3.

Bayesian coestimation of phylogeny and sequence alignment.

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

BMC Bioinformatics. 2005 Apr 1;6:83.

4.

Ancestral sequence alignment under optimal conditions.

Hudek AK, Brown DG.

BMC Bioinformatics. 2005 Nov 17;6:273.

5.

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
6.

On the inference of parsimonious indel evolutionary scenarios.

Chindelevitch L, Li Z, Blais E, Blanchette M.

J Bioinform Comput Biol. 2006 Jun;4(3):721-44.

PMID:
16960972
8.

Treelength optimization for phylogeny estimation.

Liu K, Warnow T.

PLoS One. 2012;7(3):e33104. doi: 10.1371/journal.pone.0033104. Epub 2012 Mar 19.

9.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
10.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
11.
12.

Barking up the wrong treelength: the impact of gap penalty on alignment and tree accuracy.

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

IEEE/ACM Trans Comput Biol Bioinform. 2009 Jan-Mar;6(1):7-21. doi: 10.1109/TCBB.2008.63.

PMID:
19179695
13.

Joint Bayesian estimation of alignment and phylogeny.

Redelings BD, Suchard MA.

Syst Biol. 2005 Jun;54(3):401-18.

PMID:
16012107
14.

Ancestral maximum likelihood of evolutionary trees is hard.

Addario-Berry L, Chor B, Hallett M, Lagergren J, Panconesi A, Wareham T.

J Bioinform Comput Biol. 2004 Jun;2(2):257-71.

PMID:
15297981
15.

Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.

Berger SA, Krompass D, Stamatakis A.

Syst Biol. 2011 May;60(3):291-302. doi: 10.1093/sysbio/syr010. Epub 2011 Mar 23.

16.
17.

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.

18.

Simultaneous phylogeny reconstruction and multiple sequence alignment.

Yue F, Shi J, Tang J.

BMC Bioinformatics. 2009 Jan 30;10 Suppl 1:S11. doi: 10.1186/1471-2105-10-S1-S11.

19.

Molecular systematics of terraranas (Anura: Brachycephaloidea) with an assessment of the effects of alignment and optimality criteria.

Padial JM, Grant T, Frost DR.

Zootaxa. 2014 Jun 26;3825:1-132. doi: 10.11646/zootaxa.3825.1.1. Erratum in: Zootaxa. 2014;3827(4):599-600.

PMID:
24989881
20.

Pair hidden Markov models on tree structures.

Sakakibara Y.

Bioinformatics. 2003;19 Suppl 1:i232-40.

PMID:
12855464

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