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Results: 1 to 20 of 134

1.

Evolutionary fingerprinting of genes.

Pond SL, Scheffler K, Gravenor MB, Poon AF, Frost SD.

Mol Biol Evol. 2010 Mar;27(3):520-36. doi: 10.1093/molbev/msp260. Epub 2009 Oct 28.

PMID:
19864470
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Evolutionary rates at codon sites may be used to align sequences and infer protein domain function.

Durand PM, Hazelhurst S, Coetzer TL.

BMC Bioinformatics. 2010 Mar 24;11:151. doi: 10.1186/1471-2105-11-151.

PMID:
20334658
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

CodonTest: modeling amino acid substitution preferences in coding sequences.

Delport W, Scheffler K, Botha G, Gravenor MB, Muse SV, Kosakovsky Pond SL.

PLoS Comput Biol. 2010 Aug 19;6(8). pii: e1000885. doi: 10.1371/journal.pcbi.1000885.

PMID:
20808876
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Evolutionary models accounting for layers of selection in protein-coding genes and their impact on the inference of positive selection.

Rubinstein ND, Doron-Faigenboim A, Mayrose I, Pupko T.

Mol Biol Evol. 2011 Dec;28(12):3297-308. doi: 10.1093/molbev/msr162. Epub 2011 Jun 20.

PMID:
21690564
[PubMed - indexed for MEDLINE]
Free Article
5.

Vestige: maximum likelihood phylogenetic footprinting.

Wakefield MJ, Maxwell P, Huttley GA.

BMC Bioinformatics. 2005 May 29;6:130.

PMID:
15921531
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

GENOMEPOP: a program to simulate genomes in populations.

Carvajal-Rodríguez A.

BMC Bioinformatics. 2008 Apr 30;9:223. doi: 10.1186/1471-2105-9-223.

PMID:
18447924
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Evolutionary model selection with a genetic algorithm: a case study using stem RNA.

Kosakovsky Pond SL, Mannino FV, Gravenor MB, Muse SV, Frost SD.

Mol Biol Evol. 2007 Jan;24(1):159-70. Epub 2006 Oct 12.

PMID:
17038448
[PubMed - indexed for MEDLINE]
Free Article
8.

Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes.

Kryazhimskiy S, Bazykin GA, Dushoff J.

J Virol. 2008 May;82(10):4938-45. doi: 10.1128/JVI.02415-07. Epub 2008 Mar 5.

PMID:
18321967
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Empirical codon substitution matrix.

Schneider A, Cannarozzi GM, Gonnet GH.

BMC Bioinformatics. 2005 Jun 1;6:134.

PMID:
15927081
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Variation in evolutionary processes at different codon positions.

Bofkin L, Goldman N.

Mol Biol Evol. 2007 Feb;24(2):513-21. Epub 2006 Nov 21.

PMID:
17119011
[PubMed - indexed for MEDLINE]
Free Article
11.

The evolutionary dynamics of a rapidly mutating virus within and between hosts: the case of hepatitis C virus.

Luciani F, Alizon S.

PLoS Comput Biol. 2009 Nov;5(11):e1000565. doi: 10.1371/journal.pcbi.1000565. Epub 2009 Nov 13.

PMID:
19911046
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A combined empirical and mechanistic codon model.

Doron-Faigenboim A, Pupko T.

Mol Biol Evol. 2007 Feb;24(2):388-97. Epub 2006 Nov 16.

PMID:
17110464
[PubMed - indexed for MEDLINE]
Free Article
13.

Incorporating evolution of transcription factor binding sites into annotated alignments.

Bais AS, Grossmann S, Vingron M.

J Biosci. 2007 Aug;32(5):841-50.

PMID:
17914226
[PubMed - indexed for MEDLINE]
Free Article
14.

Patterns of evolutionary constraints on genes in humans.

De S, Lopez-Bigas N, Teichmann SA.

BMC Evol Biol. 2008 Oct 7;8:275. doi: 10.1186/1471-2148-8-275.

PMID:
18840274
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.

Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C.

Virol J. 2008 Dec 23;5:160. doi: 10.1186/1743-422X-5-160. Review.

PMID:
19105834
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Euclidian space and grouping of biological objects.

Grishin VN, Grishin NV.

Bioinformatics. 2002 Nov;18(11):1523-34.

PMID:
12424125
[PubMed - indexed for MEDLINE]
Free Article
17.

Evolution of pathogenic viruses with special reference to the rates of synonymous and nonsynonymous substitutions.

Gojobori T, Yamaguchi Y, Ikeo K, Mizokami M.

Jpn J Genet. 1994 Oct;69(5):481-8. Review.

PMID:
7999369
[PubMed - indexed for MEDLINE]
Free Article
18.

Evolutionary distance estimation and fidelity of pair wise sequence alignment.

Rosenberg MS.

BMC Bioinformatics. 2005 Apr 19;6:102.

PMID:
15840174
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Likelihood-based clustering (LiBaC) for codon models, a method for grouping sites according to similarities in the underlying process of evolution.

Bao L, Gu H, Dunn KA, Bielawski JP.

Mol Biol Evol. 2008 Sep;25(9):1995-2007. doi: 10.1093/molbev/msn145. Epub 2008 Jun 26.

PMID:
18586695
[PubMed - indexed for MEDLINE]
Free Article
20.

Rohlin distance and the evolution of influenza A virus: weak attractors and precursors.

Burioni R, Scalco R, Casartelli M.

PLoS One. 2011;6(12):e27924. doi: 10.1371/journal.pone.0027924. Epub 2011 Dec 6. Erratum in: PLoS One. 2012;7(1):doi/10.1371/annotation/289e7480-aaa8-42b5-8a24-e45030f58dca. PLoS One. 2012;7(1):doi/10.1371/annotation/bcc81b1a-608d-4814-b287-7a5ce3d7ee36.

PMID:
22162994
[PubMed - indexed for MEDLINE]
Free PMC Article

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