-
1
-
-
33847645097
-
-
Adachi J, Hasegawa M. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs 28 March
-
Adachi J, Hasegawa M. 1996. MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood. Computer Science Monographs 28 (March).
-
-
-
-
2
-
-
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
-
3
-
-
13444273448
-
-
Bairoch A, Apweiler R, Wu CH, et al. (15 co-authors). 2005. The universal protein resource (UniProt). Nucleic Acids Res. 33:D154-D159.
-
Bairoch A, Apweiler R, Wu CH, et al. (15 co-authors). 2005. The universal protein resource (UniProt). Nucleic Acids Res. 33:D154-D159.
-
-
-
-
4
-
-
9144257886
-
-
Bateman A, Coin L, Durbin R, et al. (13 co-authors). 2004. The Pfam protein families database. Nucleic Acids Res. 32:D138-D141.
-
Bateman A, Coin L, Durbin R, et al. (13 co-authors). 2004. The Pfam protein families database. Nucleic Acids Res. 32:D138-D141.
-
-
-
-
5
-
-
0027483434
-
Empirical and structural models for insertions and deletions in the divergent evolution of proteins
-
Benner SA, Cohen M, Gonnet G. 1993. Empirical and structural models for insertions and deletions in the divergent evolution of proteins. J Mol Biol. 229:1065-1082.
-
(1993)
J Mol Biol
, vol.229
, pp. 1065-1082
-
-
Benner, S.A.1
Cohen, M.2
Gonnet, G.3
-
6
-
-
85142140386
-
-
Cartwright RA. 2005. DNA assembly with gaps (DAWG): simulating sequence evolution. Bioinformatics. 21:iii31-iii38.
-
Cartwright RA. 2005. DNA assembly with gaps (DAWG): simulating sequence evolution. Bioinformatics. 21:iii31-iii38.
-
-
-
-
7
-
-
3342888069
-
Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments
-
Chang MSS, Benner SA. 2004. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol. 341:617-631.
-
(2004)
J Mol Biol
, vol.341
, pp. 617-631
-
-
Chang, M.S.S.1
Benner, S.A.2
-
8
-
-
0029934516
-
The CXXC motif: Imperatives for the formation of native disulfide bonds in the cell
-
Chivers PT, Laboissière MC, Raines RT. 1996. The CXXC motif: imperatives for the formation of native disulfide bonds in the cell. EMBO J. 15:2659-2667.
-
(1996)
EMBO J
, vol.15
, pp. 2659-2667
-
-
Chivers, P.T.1
Laboissière, M.C.2
Raines, R.T.3
-
9
-
-
0015987426
-
Prediction of protein conformation
-
Chou PY, Fasman GD. 1974. Prediction of protein conformation. Biochemistry. 13:222-245.
-
(1974)
Biochemistry
, vol.13
, pp. 222-245
-
-
Chou, P.Y.1
Fasman, G.D.2
-
10
-
-
0031743421
-
Profile hidden Markov models
-
Eddy SR. 1998. Profile hidden Markov models. Bioinformatics. 14:755-763.
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.R.1
-
11
-
-
2942544229
-
COACH: Profile-profile alignment of protein families using hidden Markov models
-
Edgar RC, Sjolander K. 2004. COACH: profile-profile alignment of protein families using hidden Markov models. Bioinformatics. 20:1309-1318.
-
(2004)
Bioinformatics
, vol.20
, pp. 1309-1318
-
-
Edgar, R.C.1
Sjolander, K.2
-
12
-
-
33847673282
-
-
Felsenstein J. 2005. PHYLIP phylogeny inference package. Version 3.65. Distributed by the author. Seattle WA, Department of Genome Sciences, University of Washington
-
Felsenstein J. 2005. PHYLIP phylogeny inference package. Version 3.65. Distributed by the author. Seattle (WA): Department of Genome Sciences, University of Washington.
-
-
-
-
13
-
-
0027506279
-
Structure and sequence relationships in the lipocalins and related proteins
-
Flower DR, North ACT, Attwood TK. 1993. Structure and sequence relationships in the lipocalins and related proteins. Protein Sci. 2:753-761.
-
(1993)
Protein Sci
, vol.2
, pp. 753-761
-
-
Flower, D.R.1
North, A.C.T.2
Attwood, T.K.3
-
14
-
-
0035130367
-
The human olfactory subgenome: From sequence to structure and evolution
-
Fuchs T, Glusman G, Horn-Saban S, Lancet D, Pilpel Y. 2001. The human olfactory subgenome: from sequence to structure and evolution. Hum Genet. 108:1-13.
-
(2001)
Hum Genet
, vol.108
, pp. 1-13
-
-
Fuchs, T.1
Glusman, G.2
Horn-Saban, S.3
Lancet, D.4
Pilpel, Y.5
-
15
-
-
33645103356
-
In silico sequence evolution with site-specific interactions along phylogenetic trees
-
Gesell T, Haeseler A. 2006. In silico sequence evolution with site-specific interactions along phylogenetic trees. Bioinformatics. 22:716-722.
-
(2006)
Bioinformatics
, vol.22
, pp. 716-722
-
-
Gesell, T.1
Haeseler, A.2
-
16
-
-
14644399312
-
A comparison of human and chimpanzee olfactory receptor gene repertoires
-
Gilad Y, Man O, Glusman G. 2005. A comparison of human and chimpanzee olfactory receptor gene repertoires. Genome Res. 15:224-230.
-
(2005)
Genome Res
, vol.15
, pp. 224-230
-
-
Gilad, Y.1
Man, O.2
Glusman, G.3
-
17
-
-
3042852894
-
Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function
-
Gooneskere NCW, Lee B. 2004. Frequency of gaps observed in a structurally aligned protein pair database suggests a simple gap penalty function. Nucleic Acids Res. 32:2838-2843.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 2838-2843
-
-
Gooneskere, N.C.W.1
Lee, B.2
-
18
-
-
0030670413
-
PSeq-Gen: An application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees
-
Grassly NC, Adachi J, Rambaut A. 1997. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:559-560.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 559-560
-
-
Grassly, N.C.1
Adachi, J.2
Rambaut, A.3
-
19
-
-
14544277657
-
Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences
-
Hall BG. 2004. Comparison of the accuracies of several phylogenetic methods using protein and DNA sequences. Mol Biol Evol. 22:792-802.
-
(2004)
Mol Biol Evol
, vol.22
, pp. 792-802
-
-
Hall, B.G.1
-
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
-
21
-
-
0033578684
-
Protein secondary structure prediction based on position-specific scoring matrices
-
Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol. 292:195-202.
-
(1999)
J Mol Biol
, vol.292
, pp. 195-202
-
-
Jones, D.T.1
-
22
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame C, Higgins DG, Heringa J. 2000. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-217.
-
(2000)
J Mol Biol
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
23
-
-
15244362640
-
Structural similarity of loops in protein families: Toward the understanding of protein evolution
-
Panchenko AR, Madej T. 2005. Structural similarity of loops in protein families: toward the understanding of protein evolution. BMC Evol Biol. 5:10.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 10
-
-
Panchenko, A.R.1
Madej, T.2
-
24
-
-
27644471132
-
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
-
Pang A, Smith AD, Nuin PAS, Tillier ERM. 2005. SIMPROT: using an empirically determined indel distribution in simulations of protein evolution. BMC Bioinformatics. 6:236.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 236
-
-
Pang, A.1
Smith, A.D.2
Nuin, P.A.S.3
Tillier, E.R.M.4
-
26
-
-
0030928378
-
Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
-
Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
-
(1997)
Comput Appl Biosci
, vol.13
, pp. 235-238
-
-
Rambaut, A.1
Grassly, N.C.2
-
27
-
-
28544438123
-
MySSP: Non-stationary evolutionary sequence simulation, including indels
-
Rosenberg MS. 2005. MySSP: non-stationary evolutionary sequence simulation, including indels. Evol Bioinform Online. 1:81-83.
-
(2005)
Evol Bioinform Online
, vol.1
, pp. 81-83
-
-
Rosenberg, M.S.1
-
28
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 4:406-425.
-
(1987)
Mol Biol Evol
, vol.4
, pp. 406-425
-
-
Saitou, N.1
Nei, M.2
-
30
-
-
0031857684
-
Rose: Generating sequence families
-
Stoye J, Evers D, Meyer F. 1998. Rose: generating sequence families. Bioinformatics. 14:157-163.
-
(1998)
Bioinformatics
, vol.14
, pp. 157-163
-
-
Stoye, J.1
Evers, D.2
Meyer, F.3
-
31
-
-
33847613600
-
-
Swofford D. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods, Version 4. Sunderland MA, Sinauer Associates
-
Swofford D. 2003. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland (MA): Sinauer Associates.
-
-
-
-
32
-
-
0033674329
-
Models of protein sequence evolution and their applications
-
Thorne J. 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.1
-
33
-
-
0034786532
-
The HMMTOP transmembrane topology prediction server
-
Tusnady GE, Simon I. 2001. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:849-850.
-
(2001)
Bioinformatics
, vol.17
, pp. 849-850
-
-
Tusnady, G.E.1
Simon, I.2
-
34
-
-
0036135450
-
Protein structure, neighbor effect, and a new index of amino acid dissimilarities
-
Xia X, Xie Z. 2002. Protein structure, neighbor effect, and a new index of amino acid dissimilarities. Mol Biol Evol. 19:58-67.
-
(2002)
Mol Biol Evol
, vol.19
, pp. 58-67
-
-
Xia, X.1
Xie, Z.2
-
35
-
-
0027132974
-
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
-
Yang Z. 1993. Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 10:1396-1401.
-
(1993)
Mol Biol Evol
, vol.10
, pp. 1396-1401
-
-
Yang, Z.1
-
36
-
-
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
|