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Results: 1 to 20 of 134

1.

Comparison of three methods for estimating rates of synonymous and nonsynonymous nucleotide substitutions.

Tzeng YH, Pan R, Li WH.

Mol Biol Evol. 2004 Dec;21(12):2290-8. Epub 2004 Aug 25.

PMID:
15329386
[PubMed - indexed for MEDLINE]
Free Article
2.

New methods for estimating the numbers of synonymous and nonsynonymous substitutions.

Ina Y.

J Mol Evol. 1995 Feb;40(2):190-226.

PMID:
7699723
[PubMed - indexed for MEDLINE]
3.

Computing Ka and Ks with a consideration of unequal transitional substitutions.

Zhang Z, Li J, Yu J.

BMC Evol Biol. 2006 Jun 2;6:44.

PMID:
16740169
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Codon substitution in evolution and the "saturation" of synonymous changes.

Gojobori T.

Genetics. 1983 Dec;105(4):1011-27.

PMID:
6642197
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable substitution rates.

Wang DP, Wan HL, Zhang S, Yu J.

Biol Direct. 2009 Jun 16;4:20. doi: 10.1186/1745-6150-4-20.

PMID:
19531225
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Not so different after all: a comparison of methods for detecting amino acid sites under selection.

Kosakovsky Pond SL, Frost SD.

Mol Biol Evol. 2005 May;22(5):1208-22. Epub 2005 Feb 9.

PMID:
15703242
[PubMed - indexed for MEDLINE]
Free Article
7.

Towards realistic codon models: among site variability and dependency of synonymous and non-synonymous rates.

Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T.

Bioinformatics. 2007 Jul 1;23(13):i319-27.

PMID:
17646313
[PubMed - indexed for MEDLINE]
Free Article
8.
9.

Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

Yang Z, Nielsen R.

Mol Biol Evol. 2000 Jan;17(1):32-43.

PMID:
10666704
[PubMed - indexed for MEDLINE]
Free Article
10.

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

Aris-Brosou S, Bielawski JP.

Gene. 2006 Aug 15;378:58-64. Epub 2006 May 22.

PMID:
16797879
[PubMed - indexed for MEDLINE]
11.

Evaluation of six methods for estimating synonymous and nonsynonymous substitution rates.

Zhang Z, Yu J.

Genomics Proteomics Bioinformatics. 2006 Aug;4(3):173-81.

PMID:
17127215
[PubMed - indexed for MEDLINE]
Free Article
12.

A codon-based model of nucleotide substitution for protein-coding DNA sequences.

Goldman N, Yang Z.

Mol Biol Evol. 1994 Sep;11(5):725-36.

PMID:
7968486
[PubMed - indexed for MEDLINE]
13.
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15.

A method for estimating the numbers of synonymous and nonsynonymous substitutions per site.

Comeron JM.

J Mol Evol. 1995 Dec;41(6):1152-9.

PMID:
8587111
[PubMed - indexed for MEDLINE]
16.

Empirical analysis of the most relevant parameters of codon substitution models.

Zoller S, Schneider A.

J Mol Evol. 2010 Jun;70(6):605-12. doi: 10.1007/s00239-010-9356-9. Epub 2010 Jun 5.

PMID:
20526712
[PubMed - indexed for MEDLINE]
17.

Substitution rates in Drosophila nuclear genes: implications for translational selection.

Dunn KA, Bielawski JP, Yang Z.

Genetics. 2001 Jan;157(1):295-305.

PMID:
11139510
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A codon-based model designed to describe lentiviral evolution.

Pedersen AK, Wiuf C, Christiansen FB.

Mol Biol Evol. 1998 Aug;15(8):1069-81.

PMID:
9718734
[PubMed - indexed for MEDLINE]
Free Article
19.

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions.

Nei M, Gojobori T.

Mol Biol Evol. 1986 Sep;3(5):418-26.

PMID:
3444411
[PubMed - indexed for MEDLINE]
20.

An empirical codon model for protein sequence evolution.

Kosiol C, Holmes I, Goldman N.

Mol Biol Evol. 2007 Jul;24(7):1464-79. Epub 2007 Mar 30. Erratum in: Mol Biol Evol. 2007 Sep;24(9):2151.

PMID:
17400572
[PubMed - indexed for MEDLINE]
Free Article
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