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Items: 1 to 20 of 392

1.

Bayesian gene/species tree reconciliation and orthology analysis using MCMC.

Arvestad L, Berglund AC, Lagergren J, Sennblad B.

Bioinformatics. 2003;19 Suppl 1:i7-15.

PMID:
12855432
2.

Probabilistic orthology analysis.

Sennblad B, Lagergren J.

Syst Biol. 2009 Aug;58(4):411-24. doi: 10.1093/sysbio/syp046. Epub 2009 Aug 18.

PMID:
20525594
3.

Integrating Sequence Evolution into Probabilistic Orthology Analysis.

Ullah I, Sjöstrand J, Andersson P, Sennblad B, Lagergren J.

Syst Biol. 2015 Nov;64(6):969-82. doi: 10.1093/sysbio/syv044. Epub 2015 Jun 30.

PMID:
26130236
4.

Bayesian coestimation of phylogeny and sequence alignment.

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

BMC Bioinformatics. 2005 Apr 1;6:83.

5.
6.

Estimating species trees using multiple-allele DNA sequence data.

Liu L, Pearl DK, Brumfield RT, Edwards SV.

Evolution. 2008 Aug;62(8):2080-91. doi: 10.1111/j.1558-5646.2008.00414.x. Epub 2008 May 5.

PMID:
18462214
8.

An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework.

Doyon JP, Hamel S, Chauve C.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jan-Feb;9(1):26-39. doi: 10.1109/TCBB.2011.64. Epub 2011 Mar 30.

PMID:
21464510
9.

Identifiability of parameters in MCMC Bayesian inference of phylogeny.

Rannala B.

Syst Biol. 2002 Oct;51(5):754-60.

PMID:
12396589
10.

Detecting recombination with MCMC.

Husmeier D, McGuire G.

Bioinformatics. 2002;18 Suppl 1:S345-53.

PMID:
12169565
11.
12.

Orthology prediction at scalable resolution by phylogenetic tree analysis.

van der Heijden RT, Snel B, van Noort V, Huynen MA.

BMC Bioinformatics. 2007 Mar 8;8:83.

13.

Exploring fast computational strategies for probabilistic phylogenetic analysis.

Rodrigue N, Philippe H, Lartillot N.

Syst Biol. 2007 Oct;56(5):711-26.

PMID:
17849326
14.

Detecting correlation between characters in a comparative analysis with uncertain phylogeny.

Huelsenbeck JP, Rannala B.

Evolution. 2003 Jun;57(6):1237-47.

PMID:
12894932
15.

Bayesian estimation of concordance among gene trees.

Ané C, Larget B, Baum DA, Smith SD, Rokas A.

Mol Biol Evol. 2007 Feb;24(2):412-26. Epub 2006 Nov 9. Erratum in: Mol Biol Evol. 2007 Jul;24(7):1575.

PMID:
17095535
16.

Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times.

dos Reis M, Yang Z.

Mol Biol Evol. 2011 Jul;28(7):2161-72. doi: 10.1093/molbev/msr045. Epub 2011 Feb 10.

PMID:
21310946
17.

A probabilistic method to detect regulatory modules.

Sinha S, van Nimwegen E, Siggia ED.

Bioinformatics. 2003;19 Suppl 1:i292-301.

PMID:
12855472
19.

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.

Akerborg O, Sennblad B, Arvestad L, Lagergren J.

Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5714-9. doi: 10.1073/pnas.0806251106. Epub 2009 Mar 19.

20.

Phylogenetic MCMC algorithms are misleading on mixtures of trees.

Mossel E, Vigoda E.

Science. 2005 Sep 30;309(5744):2207-9.

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