Models for
variable selection pressure among sites:
Bao L, Gu H, Dunn KA, Bielawski JP. 2008. Likelihood Based
Clustering (LiBaC) for Codon Models, a method for grouping sites
according to similarities in the underlying process of evolution.
Mol Biol Evol. Jun 26. [Epub ahead of print]
Mayrose I, Doron-Faigenboim A, Bacharach E, Pupko T. 2007.
Towards realistic codon models: among site variability and
dependency of synonymous and non-synonymous rates. Bioinformatics.
23(13):i319-27.
Bao L, Gu H, Dunn KA, Bielawski JP. 2007. Methods for selecting
fixed-effect models for heterogeneous codon evolution, with
comments on their application to gene and genome data. BMC Evol
Biol. 7 Suppl 1:S5.
Wilson DJ, McVean G. 2006. Estimating
diversifying selection and functional constraint in the presence
of recombination. Genetics. 172(3):1411-1125.
Huelsenbeck JP, Jain S, Frost SW, Pond SL. 2006.
A Dirichlet process model for detecting positive
selection in protein-coding DNA sequences. Proc Natl Acad Sci U S
A. 103(16):6263-6268.
Pond SK, Muse SV. 2005. Site-to-site
variation of synonymous substitution rates. Mol Biol Evol.
22(12):2375-85.
Massingham T, Goldman N. 2005. Detecting amino acid sites under
positive selection and purifying selection. Genetics.
169(3):1753-1762.
Huelsenbeck JP, Dyer KA. 2004. Bayesian estimation of positively
selected sites. J Mol Evol. 58:661-672.
Yang, Z., and W. J. Swanson. 2002.
Codon-substitution models to detect adaptive evolution that
account for heterogeneous selective pressures among site classes.
Mol. Biol. Evol. 19:49-57.
Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000.
Codon-substitution models for heterogeneous selection pressure at
amino acid sites. Genetics 155:431-449.
Nielsen, R. and Z. Yang. 1998. Likelihood models for detecting
positively selected amino acid sites and applications to the HIV-1
envelope gene. Genetics 148:929-936.
Models for
variation in selection pressure among lineages:
Kosakovsky Pond SL, Frost SD. 2005. A
genetic algorithm approach to detecting lineage-specific variation
in selection pressure. Mol Biol Evol. 22(3):478-485.
Seo TK, Kishino H, Thorne JL. 2004. Estimating
absolute rates of synonymous and nonsynonymous nucleotide
substitution in order to characterize natural selection and date
species divergences. Mol Biol Evol. 21(7):1201-1213.
Bielawski, J. P. and Z. Yang. 2003. Maximum likelihood methods
for detecting adaptive evolution after gene duplication. Journal
of Structural and Functional Genomics, 3:201-212.
Yang, Z. 1998. Likelihood ratio tests for detecting positive
selection and application to primate lysozyme evolution. Mol.
Biol. Evol. 15:568-573.
Models for
variable selection pressure among sites & lineages:
Zhang J, Nielsen R, Yang Z. 2005. Evaluation
of an improved branch-site likelihood method for detecting
positive selection at the molecular level. Mol Biol Evol.
22(12):2472-2479.
Bielawski, J. P. and Z. Yang. 2004. A maximum likelihood method
for detecting functional divergence at individual codon sites,
with application to gene family evolution. Journal of Molecular
Evolution, 59:121-132.
Guindon S, Rodrigo AG, Dyer KA, Huelsenbeck JP. 2004. Modeling
the site-specific variation of selection patterns along lineages.
Proc Natl Acad Sci U S A. 101:12957-12962.
Forsberg R, Christiansen FB.
2003. A codon-based model of host-specific selection in
parasites, with an application to the influenza A virus. Mol Biol
Evol. 20(8):1252-1259.
Yang Z, Nielsen R. 2002. Codon-substitution models for detecting
molecular adaptation at individual sites along specific lineages.
Mol Biol Evol. 19:908-917.
Yet more
models:
Yang Z, Nielsen R. 2008. Mutation-selection
models of codon substitution and their use to estimate selective
strengths on codon usage. Mol Biol Evol. 25(3):568-579.
Kosakovsky Pond SL, Poon AF, Leigh Brown AJ, Frost SD.
2008. A Maximum Likelihood Method for Detecting
Directional Evolution in Protein Sequences and its Application to
Influenza A Virus. Mol Biol Evol. 2008 May 29. [Epub ahead of
print]
Seoighe C, Ketwaroo F, Pillay V, Scheffler K, Wood N, Duffet R,
Zvelebil M, Martinson N, McIntyre J, Morris L, Hide W. 2007.
A model of directional selection applied to the evolution
of drug resistance in HIV-1. Mol Biol Evol. 24(4):1025-1031.
Doron-Faigenboim A, Pupko T. 2008. A
combined empirical and mechanistic codon model. Mol Biol Evol.
24(2):388-397.
Kosiol C, Holmes I, Goldman N. 2007. An
empirical codon model for protein sequence evolution. Mol Biol
Evol. 24(7):1464-1479.
Wong WS, Sainudiin R, Nielsen R. 2006.
Identification of physicochemical selective pressure on protein
encoding nucleotide sequences. BMC Bioinformatics. 7:148.
Sainudiin R, Wong WS, Yogeeswaran K, Nasrallah JB, Yang Z,
Nielsen R. 2005. Detecting
site-specific physicochemical selective pressures: applications to
the Class I HLA of the human major histocompatibility complex and
the SRK of the plant sporophytic self-incompatibility system. J
Mol Evol. 60(3):315-26.
Schneider A, Cannarozzi GM, Gonnet GH. 2005.
Empirical codon substitution matrix. BMC Bioinformatics.
6:134.
Yang, Z., R. Nielsen, and M. Hasegawa. 1998. Models of amino acid
substitution and applications to mitochondrial protein evolution.
Molecular Biology and Evolution 15:1600-1611.