-
1
-
-
0029974748
-
Model of amino acid substitution in proteins encoded by mitochondrial DNA
-
Adachi J, Hasegawa M (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol 42:459-468
-
(1996)
J Mol Evol
, vol.42
, pp. 459-468
-
-
Adachi, J.1
Hasegawa, M.2
-
2
-
-
0029999739
-
A Bayesian evolutionary distance for parametrically aligned sequences
-
Agarwal P, States DJ (1996) A Bayesian evolutionary distance for parametrically aligned sequences. J Comput Biol 3:1-17
-
(1996)
J Comput Biol
, vol.3
, pp. 1-17
-
-
Agarwal, P.1
States, D.J.2
-
3
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
4
-
-
0031453046
-
Estimation of reversible substitution matrices from multiple pairs of sequences
-
Arvestad L, Bruno WJ (1997) Estimation of reversible substitution matrices from multiple pairs of sequences. J Mol Evol 45:696-703
-
(1997)
J Mol Evol
, vol.45
, pp. 696-703
-
-
Arvestad, L.1
Bruno, W.J.2
-
5
-
-
0011542799
-
The Pfam protein families database
-
Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL (2002) The Pfam protein families database. Nucleic Acids Res 30:276-280
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 276-280
-
-
Bateman, A.1
Birney, E.2
Cerruti, L.3
Durbin, R.4
Etwiller, L.5
Eddy, S.R.6
Griffiths-Jones, S.7
Howe, K.L.8
Marshall, M.9
Sonnhammer, E.L.10
-
6
-
-
0022358402
-
Evolutionary trees from nucleic acid and protein sequences
-
Bishop M, Friday A (1985) Evolutionary trees from nucleic acid and protein sequences. Proc R Soc Lond B 226:272-302
-
(1985)
Proc R Soc Lond B
, vol.226
, pp. 272-302
-
-
Bishop, M.1
Friday, A.2
-
7
-
-
0028172520
-
Phylogenetic relationships among eutharian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene
-
Cao Y, Adachi J, Janke A, Pääbo S, Hasegawa M (1994) Phylogenetic relationships among eutharian orders estimated from inferred sequences of mitochondrial proteins: Instability of a tree based on a single gene. J Mol Evol 39:519-527
-
(1994)
J Mol Evol
, vol.39
, pp. 519-527
-
-
Cao, Y.1
Adachi, J.2
Janke, A.3
Pääbo, S.4
Hasegawa, M.5
-
8
-
-
0002929101
-
A model of evolutionary change in proteins
-
Dayhoff MO (ed) National Biomedical Research Foundation, Washington, D.C.
-
Dayhoff MO, Eck RV, Park CM (1972) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, National Biomedical Research Foundation, Washington, D.C., vol 5, pp 89-99
-
(1972)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 89-99
-
-
Dayhoff, M.O.1
Eck, R.V.2
Park, C.M.3
-
9
-
-
0034786417
-
Rate matrices for analyzing large families of protein sequences
-
Devauchelle C, Grossmann A, Hénaut A, Holschneider M, Monnerot M, Risler J, Torrésani B (2001) Rate matrices for analyzing large families of protein sequences. J Comput Biol 8:381-399
-
(2001)
J Comput Biol
, vol.8
, pp. 381-399
-
-
Devauchelle, C.1
Grossmann, A.2
Hénaut, A.3
Holschneider, M.4
Monnerot, M.5
Risler, J.6
Torrésani, B.7
-
11
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
-
(1981)
J Mol Evol
, vol.17
, pp. 368-376
-
-
Felsenstein, J.1
-
13
-
-
0036856275
-
A novel use of equilibrium frequencies in models of sequence evolution
-
Goldman N, Whelan S (2002) A novel use of equilibrium frequencies in models of sequence evolution. Mol Biol Evol 19:1821-1831
-
(2002)
Mol Biol Evol
, vol.19
, pp. 1821-1831
-
-
Goldman, N.1
Whelan, S.2
-
14
-
-
0030601801
-
Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses
-
Goldman N, Thorne JL, Jones DT (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J Mol Biol 263:196-208
-
(1996)
J Mol Biol
, vol.263
, pp. 196-208
-
-
Goldman, N.1
Thorne, J.L.2
Jones, D.T.3
-
16
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
Gonnet GH, Cohen M, Benner S (1992) Exhaustive matching of the entire protein sequence database. Science 256:1443-1445
-
(1992)
Science
, vol.256
, pp. 1443-1445
-
-
Gonnet, G.H.1
Cohen, M.2
Benner, S.3
-
18
-
-
0026458378
-
Amino acid substitution matrices from protein blocks
-
USA
-
Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919
-
(1992)
Proc Natl Acad Sci
, vol.89
, pp. 10915-10919
-
-
Henikoff, S.1
Henikoff, J.G.2
-
19
-
-
0036298990
-
An expectation maximization algorithm for training hidden substitution models
-
Holmes I, Rubin GM (2002) An expectation maximization algorithm for training hidden substitution models. J Mol Biol 317:753-764
-
(2002)
J Mol Biol
, vol.317
, pp. 753-764
-
-
Holmes, I.1
Rubin, G.M.2
-
20
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
-
(1992)
Comput Appl Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
23
-
-
0028808763
-
Context-dependent optimal substitution matrices
-
Koshi JM, Goldstein RA (1995) Context-dependent optimal substitution matrices. Protein Eng 8:641-645
-
(1995)
Protein Eng
, vol.8
, pp. 641-645
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
24
-
-
0029881442
-
Probabilistic reconstruction of ancestral protein sequences
-
Koshi JM, Goldstein RA (1996) Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 42:313-320
-
(1996)
J Mol Evol
, vol.42
, pp. 313-320
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
25
-
-
0021277009
-
A new method for calculating evolutionary substitution rates
-
Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86-93
-
(1984)
J Mol Evol
, vol.20
, pp. 86-93
-
-
Lanave, C.1
Preparata, G.2
Saccone, C.3
Serio, G.4
-
26
-
-
0036213764
-
Modeling mitochondrial protein evolution using structural information
-
Liò P, Goldman N (2002) Modeling mitochondrial protein evolution using structural information. J Mol Evol 54:519-529
-
(2002)
J Mol Evol
, vol.54
, pp. 519-529
-
-
Liò, P.1
Goldman, N.2
-
27
-
-
0031788749
-
PASSML: Combining evolutionary inference and protein secondary structure prediction
-
Liò P, Goldman N, Thorne JL, Jones DT (1998) PASSML: combining evolutionary inference and protein secondary structure prediction. Bioinformatics 14:726-733
-
(1998)
Bioinformatics
, vol.14
, pp. 726-733
-
-
Liò, P.1
Goldman, N.2
Thorne, J.L.3
Jones, D.T.4
-
28
-
-
0034922289
-
Modeling amino acid replacement
-
Müller T, Vingron M (2000) Modeling amino acid replacement. J Comput Biol 7:761-776
-
(2000)
J Comput Biol
, vol.7
, pp. 761-776
-
-
Müller, T.1
Vingron, M.2
-
29
-
-
0036134748
-
Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
-
Müller T, Spang R, Vingron M (2002) Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. Mol Biol Evol 19:8-13
-
(2002)
Mol Biol Evol
, vol.19
, pp. 8-13
-
-
Müller, T.1
Spang, R.2
Vingron, M.3
-
30
-
-
0023989064
-
Improved tools for biological sequence comparison
-
USA
-
Pearson W, Lipman DJ (1988) Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85:2444-2448
-
(1988)
Proc Natl Acad Sci
, vol.85
, pp. 2444-2448
-
-
Pearson, W.1
Lipman, D.J.2
-
31
-
-
0033582946
-
Coevolving protein residues: Maximum likelihood identification and relationship to structure
-
Pollock D, Taylor W, Goldman N (1999) Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol 287:187-198
-
(1999)
J Mol Biol
, vol.287
, pp. 187-198
-
-
Pollock, D.1
Taylor, W.2
Goldman, N.3
-
32
-
-
0035350525
-
A test of amino acid reversibility
-
Smith NG, Eyre-Walker A (2001) A test of amino acid reversibility. J Mol Evol 52:467-469
-
(2001)
J Mol Evol
, vol.52
, pp. 467-469
-
-
Smith, N.G.1
Eyre-Walker, A.2
-
33
-
-
0033043696
-
Is there a phylogenetic signal in prokaryote proteins?
-
Teichmann S, Mitchison G (1999) Is there a phylogenetic signal in prokaryote proteins? J Mol Evol 49:98-107
-
(1999)
J Mol Evol
, vol.49
, pp. 98-107
-
-
Teichmann, S.1
Mitchison, G.2
-
34
-
-
0033674329
-
Models of protein sequence evolution and their applications
-
Thorne JL (2000) Models of protein sequence evolution and their applications. Curr Opin Genet Dev 10:602-605
-
(2000)
Curr Opin Genet Dev
, vol.10
, pp. 602-605
-
-
Thorne, J.L.1
-
35
-
-
0742286995
-
A transition probability model for amino acid substitutions from blocks
-
Veerassamy S, Smith A, Tillier ER (2003) A transition probability model for amino acid substitutions from blocks. J Comput Biol 10:997-1010
-
(2003)
J Comput Biol
, vol.10
, pp. 997-1010
-
-
Veerassamy, S.1
Smith, A.2
Tillier, E.R.3
-
36
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan S, Goldman N (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 18:691-699
-
(2001)
Mol Biol Evol
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
37
-
-
0041385962
-
PANDIT: A database of protein and associated nucleotide domains with inferred trees
-
Whelan S, de Bakker PI, Goldman N (2003) PANDIT: a database of protein and associated nucleotide domains with inferred trees. Bioinformatics 19:1556-1563
-
(2003)
Bioinformatics
, vol.19
, pp. 1556-1563
-
-
Whelan, S.1
De Bakker, P.I.2
Goldman, N.3
-
38
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
39
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang Z, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141:1641-1650
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
40
-
-
0346734129
-
The compositional adjustment of amino acid substitution matrices
-
USA
-
Yu Y, Wootton J, Altschul S (2003) The compositional adjustment of amino acid substitution matrices. Proc Natl Acad Sci USA 100:15688-15693
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 15688-15693
-
-
Yu, Y.1
Wootton, J.2
Altschul, S.3
|