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Items: 1 to 20 of 407

1.

DNA assembly with gaps (Dawg): simulating sequence evolution.

Cartwright RA.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.

PMID:
16306390
2.

Using evolutionary Expectation Maximization to estimate indel rates.

Holmes I.

Bioinformatics. 2005 May 15;21(10):2294-300. Epub 2005 Feb 24.

PMID:
15731213
3.

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
4.
5.

Indel seeds for homology search.

Mak D, Gelfand Y, Benson G.

Bioinformatics. 2006 Jul 15;22(14):e341-9.

PMID:
16873491
6.

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
7.

Statistical alignment based on fragment insertion and deletion models.

Metzler D.

Bioinformatics. 2003 Mar 1;19(4):490-9.

PMID:
12611804
8.

Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment.

Kim J, Sinha S.

Bioinformatics. 2007 Feb 1;23(3):289-97. Epub 2006 Nov 15.

PMID:
17110370
9.

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.

10.

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
11.
12.

In silico sequence evolution with site-specific interactions along phylogenetic trees.

Gesell T, von Haeseler A.

Bioinformatics. 2006 Mar 15;22(6):716-22. Epub 2005 Dec 6.

PMID:
16332711
13.

Patterns and relative rates of nucleotide and insertion/deletion evolution at six chloroplast intergenic regions in new world species of the Lecythidaceae.

Hamilton MB, Braverman JM, Soria-Hernanz DF.

Mol Biol Evol. 2003 Oct;20(10):1710-21. Epub 2003 Jun 27.

PMID:
12832633
14.

Evolution and phylogenetic utility of alignment gaps within intron sequences of three nuclear genes in bumble bees (Bombus).

Kawakita A, Sota T, Ascher JS, Ito M, Tanaka H, Kato M.

Mol Biol Evol. 2003 Jan;20(1):87-92.

PMID:
12519910
16.

Parallel rate heterogeneity in chloroplast and mitochondrial genomes of Brazil nut trees (Lecythidaceae) is consistent with lineage effects.

Soria-Hernanz DF, Braverman JM, Hamilton MB.

Mol Biol Evol. 2008 Jul;25(7):1282-96. doi: 10.1093/molbev/msn074. Epub 2008 Apr 2.

PMID:
18385219
17.

Joint Bayesian estimation of alignment and phylogeny.

Redelings BD, Suchard MA.

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

PMID:
16012107
18.

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.

19.

Indel evolution of mammalian introns and the utility of non-coding nuclear markers in eutherian phylogenetics.

Matthee CA, Eick G, Willows-Munro S, Montgelard C, Pardini AT, Robinson TJ.

Mol Phylogenet Evol. 2007 Mar;42(3):827-37. Epub 2006 Oct 11.

PMID:
17101283
20.

Empirical models for substitution in ribosomal RNA.

Smith AD, Lui TW, Tillier ER.

Mol Biol Evol. 2004 Mar;21(3):419-27. Epub 2003 Dec 5.

PMID:
14660689

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