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Items: 1 to 20 of 69

1.

MtArt: a new model of amino acid replacement for Arthropoda.

Abascal F, Posada D, Zardoya R.

Mol Biol Evol. 2007 Jan;24(1):1-5. Epub 2006 Oct 16.

PMID:
17043087
2.

A site- and time-heterogeneous model of amino acid replacement.

Blanquart S, Lartillot N.

Mol Biol Evol. 2008 May;25(5):842-58. doi: 10.1093/molbev/msn018. Epub 2008 Jan 29.

PMID:
18234708
3.

MtPAN(3): site-class specific amino acid replacement matrices for mitochondrial proteins of Pancrustacea and Collembola.

Nardi F, Liò P, Carapelli A, Frati F.

Mol Phylogenet Evol. 2014 Jun;75:239-44. doi: 10.1016/j.ympev.2014.02.001. Epub 2014 Feb 10.

PMID:
24525199
4.

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny.

Wang HC, Li K, Susko E, Roger AJ.

BMC Evol Biol. 2008 Dec 16;8:331. doi: 10.1186/1471-2148-8-331.

5.

Phylogenetic mixture models for proteins.

Le SQ, Lartillot N, Gascuel O.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):3965-76. doi: 10.1098/rstb.2008.0180.

6.

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.

Lartillot N, Philippe H.

Mol Biol Evol. 2004 Jun;21(6):1095-109. Epub 2004 Mar 10.

PMID:
15014145
7.

Modeling mitochondrial protein evolution using structural information.

Liò P, Goldman N.

J Mol Evol. 2002 Apr;54(4):519-29.

PMID:
11956690
8.

Synonymous substitutions substantially improve evolutionary inference from highly diverged proteins.

Seo TK, Kishino H.

Syst Biol. 2008 Jun;57(3):367-77. doi: 10.1080/10635150802158670.

PMID:
18570032
9.

The role of 3' UTRs in the mechanisms for segregating mitochondrial proteins.

Pattini L, Cerutti S.

IEEE Trans Nanobioscience. 2003 Dec;2(4):233-8.

PMID:
15376913
10.

Mitochondrial nucleoids from the yeast Candida parapsilosis: expansion of the repertoire of proteins associated with mitochondrial DNA.

Miyakawa I, Okamuro A, Kinsky S, Visacka K, Tomaska L, Nosek J.

Microbiology. 2009 May;155(Pt 5):1558-68. doi: 10.1099/mic.0.027474-0. Epub 2009 Apr 21.

PMID:
19383705
11.

On reduced amino acid alphabets for phylogenetic inference.

Susko E, Roger AJ.

Mol Biol Evol. 2007 Sep;24(9):2139-50. Epub 2007 Jul 25.

PMID:
17652333
12.
13.

A new criterion and method for amino acid classification.

Kosiol C, Goldman N, Buttimore NH.

J Theor Biol. 2004 May 7;228(1):97-106.

PMID:
15064085
14.

Spatial and temporal heterogeneity in nucleotide sequence evolution.

Whelan S.

Mol Biol Evol. 2008 Aug;25(8):1683-94. doi: 10.1093/molbev/msn119. Epub 2008 May 22.

PMID:
18502771
15.

Measuring the fit of sequence data to phylogenetic model: allowing for missing data.

Waddell PJ.

Mol Biol Evol. 2005 Mar;22(3):395-401. Epub 2004 Oct 6. Erratum in: Mol Biol Evol. 2005 Apr;22(4):1157.

PMID:
15470228
16.

Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates.

Kitazoe Y, Kishino H, Hasegawa M, Nakajima N, Thorne JL, Tanaka M.

PLoS One. 2008 Oct 6;3(10):e3343. doi: 10.1371/journal.pone.0003343.

17.

An improved general amino acid replacement matrix.

Le SQ, Gascuel O.

Mol Biol Evol. 2008 Jul;25(7):1307-20. doi: 10.1093/molbev/msn067. Epub 2008 Mar 26.

PMID:
18367465
18.

Different versions of the Dayhoff rate matrix.

Kosiol C, Goldman N.

Mol Biol Evol. 2005 Feb;22(2):193-9. Epub 2004 Oct 13.

PMID:
15483331
19.

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
20.

Phylogenetic and structural analysis of mitochondrial complex I proteins.

Liò P.

Gene. 2005 Jan 17;345(1):55-64. Epub 2004 Dec 29.

PMID:
15716089

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