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Items: 1 to 20 of 60

1.

Computer programs and methodologies for the simulation of DNA sequence data with recombination.

Arenas M.

Front Genet. 2013 Feb 1;4:9. doi: 10.3389/fgene.2013.00009. eCollection 2013.

2.

Critical assessment of coalescent simulators in modeling recombination hotspots in genomic sequences.

Yang T, Deng HW, Niu T.

BMC Bioinformatics. 2014 Jan 3;15:3. doi: 10.1186/1471-2105-15-3.

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.

[Foundations of the new phylogenetics].

Pavlinov IIa.

Zh Obshch Biol. 2004 Jul-Aug;65(4):334-66. Russian.

PMID:
15490579
6.

MultiSeq: unifying sequence and structure data for evolutionary analysis.

Roberts E, Eargle J, Wright D, Luthey-Schulten Z.

BMC Bioinformatics. 2006 Aug 16;7:382.

7.

GARD: a genetic algorithm for recombination detection.

Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SD.

Bioinformatics. 2006 Dec 15;22(24):3096-8. Epub 2006 Nov 16.

PMID:
17110367
8.

Consequences of recombination on traditional phylogenetic analysis.

Schierup MH, Hein J.

Genetics. 2000 Oct;156(2):879-91.

9.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

10.

Simulating DNA coding sequence evolution with EvolveAGene 3.

Hall BG.

Mol Biol Evol. 2008 Apr;25(4):688-95. doi: 10.1093/molbev/msn008. Epub 2008 Jan 12.

PMID:
18192698
11.

Detecting recombination in evolving nucleotide sequences.

Chan CX, Beiko RG, Ragan MA.

BMC Bioinformatics. 2006 Sep 18;7:412.

12.

indel-Seq-Gen: a new protein family simulator incorporating domains, motifs, and indels.

Strope CL, Scott SD, Moriyama EN.

Mol Biol Evol. 2007 Mar;24(3):640-9. Epub 2006 Dec 8.

PMID:
17158778
13.

Simulation of genomes: a review.

Carvajal-Rodríguez A.

Curr Genomics. 2008 May;9(3):155-9. doi: 10.2174/138920208784340759.

14.

A graphical method for detecting recombination in phylogenetic data sets.

McGuire G, Wright F, Prentice MJ.

Mol Biol Evol. 1997 Nov;14(11):1125-31.

PMID:
9364770
15.

SIMPROT: using an empirically determined indel distribution in simulations of protein evolution.

Pang A, Smith AD, Nuin PA, Tillier ER.

BMC Bioinformatics. 2005 Sep 27;6:236.

16.

Evaluation of methods for detecting recombination from DNA sequences: computer simulations.

Posada D, Crandall KA.

Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13757-62.

17.

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs.

Dutheil J, Boussau B.

BMC Evol Biol. 2008 Sep 22;8:255. doi: 10.1186/1471-2148-8-255.

18.

PAML 4: phylogenetic analysis by maximum likelihood.

Yang Z.

Mol Biol Evol. 2007 Aug;24(8):1586-91. Epub 2007 May 4.

PMID:
17483113
19.

Detecting and Analyzing Genetic Recombination Using RDP4.

Martin DP, Murrell B, Khoosal A, Muhire B.

Methods Mol Biol. 2017;1525:433-460.

PMID:
27896731
20.

Phylogenetic methods come of age: testing hypotheses in an evolutionary context.

Huelsenbeck JP, Rannala B.

Science. 1997 Apr 11;276(5310):227-32.

PMID:
9092465

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