-
1
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
10.1016/0022-2836(70)90057-4 5420325
-
Needleman SB Wunsch CD A general method applicable to the search for similarities in the amino acid sequence of two proteins J Mol Biol 1970 48(3):443-53 10.1016/0022-2836(70)90057-4 5420325
-
(1970)
J Mol Biol
, vol.48
, Issue.3
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
2
-
-
0001642687
-
Some biological sequence metrics
-
10.1016/0001-8708(76)90202-4
-
Waterman M Smith T Beyer W Some biological sequence metrics Advan Math 1976 20:367-387 10.1016/0001-8708(76)90202-4
-
(1976)
Advan Math
, vol.20
, pp. 367-387
-
-
Waterman, M.1
Smith, T.2
Beyer, W.3
-
3
-
-
0019887799
-
Identification of common molecular subsequences
-
10.1016/0022-2836(81)90087-5 7265238
-
Smith TF Waterman MS Identification of common molecular subsequences J Mol Biol 1981 147:195-7 10.1016/0022-2836(81)90087-5 7265238
-
(1981)
J Mol Biol
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
4
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
10.1016/0022-2836(82)90398-9 7166760
-
Gotoh O An improved algorithm for matching biological sequences J Mol Biol 1982 162:705-708 10.1016/0022-2836(82)90398-9 7166760
-
(1982)
J Mol Biol
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
5
-
-
0028464982
-
Parametric and ensemble sequence alignment algorithms
-
Waterman M Parametric and ensemble sequence alignment algorithms Bulletin of Mathematical Biology 1994 5(4):743-767
-
(1994)
Bulletin of Mathematical Biology
, vol.5
, Issue.4
, pp. 743-767
-
-
Waterman, M.1
-
7
-
-
0028181441
-
Hidden Markov models in computational biology: Applications to protein modeling
-
10.1006/jmbi.1994.1104 8107089
-
Krogh A Brown M Mian I Sjolander K Haussler D Hidden Markov models in computational biology: Applications to protein modeling J Mol Biol 1994 235:1501-1531 10.1006/jmbi.1994.1104 8107089
-
(1994)
J Mol Biol
, vol.235
, pp. 1501-1531
-
-
Krogh, A.1
Brown, M.2
Mian, I.3
Sjolander, K.4
Haussler, D.5
-
8
-
-
0026079507
-
An evolutionary model for maximum likelihood alignment of DNA sequences
-
10.1007/BF02193625 1920447
-
Thorne JL Kishino H Felsenstein J An evolutionary model for maximum likelihood alignment of DNA sequences J Mol Evol 1991 33(2):114-24 10.1007/BF02193625 1920447
-
(1991)
J Mol Evol
, vol.33
, pp. 114-124
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
9
-
-
0026528734
-
Inching toward reality: An improved likelihood model of sequence evolution
-
10.1007/BF00163848 1556741
-
Thorne JL Kishino H Felsenstein J Inching toward reality: An improved likelihood model of sequence evolution J Mol Evol 1992 34(3):16 10.1007/ BF00163848 1556741
-
(1992)
J Mol Evol
, vol.34
, Issue.3
, pp. 3-16
-
-
Thorne, J.L.1
Kishino, H.2
Felsenstein, J.3
-
10
-
-
0141869092
-
Sequence alignments and pair hidden Markov models using evolutionary history
-
10.1016/j.jmb.2003.08.015 14529629
-
Knudsen B Miyamoto M Sequence alignments and pair hidden Markov models using evolutionary history J Mol Biol 2003 333:453-460 10.1016/ j.jmb.2003.08.015 14529629
-
(2003)
J Mol Biol
, vol.333
, pp. 453-460
-
-
Knudsen, B.1
Miyamoto, M.2
-
11
-
-
1542510093
-
A 'long indel' model for evolutionary sequence alignment
-
10.1093/molbev/msh043 14694074
-
Miklós I Lunter GA Holmes I A 'long indel' model for evolutionary sequence alignment Mol Biol Evol 2004 21(3):529-540 10.1093/molbev/ msh043 14694074
-
(2004)
Mol Biol Evol
, vol.21
, Issue.3
, pp. 529-540
-
-
Miklós, I.1
Lunter, G.A.2
Holmes, I.3
-
13
-
-
0041886963
-
A hidden Markov model for progressive multiple alignment
-
10.1093/bioinformatics/btg193 12912831
-
Löytynoja A Milinkovitch M A hidden Markov model for progressive multiple alignment Bioinformatics 2003 19(12):1505-1513 10.1093/ bioinformatics/btg193 12912831
-
(2003)
Bioinformatics
, vol.19
, pp. 1505-1513
-
-
Löytynoja, A.1
Milinkovitch, M.2
-
14
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang L Jiang T On the complexity of multiple sequence alignment J Comp Biol 1994 1(4):337-348
-
(1994)
J Comp Biol
, vol.1
, Issue.4
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
15
-
-
0032438987
-
Hidden Markov Models for Detecting Remote Protein Homologies
-
10.1093/bioinformatics/14.10.846 9927713
-
Karplus K Barrett C Hughey R Hidden Markov Models for Detecting Remote Protein Homologies Bioinformatics 1998 14(10):846-856 10.1093/ bioinformatics/14.10.846 9927713
-
(1998)
Bioinformatics
, vol.14
, pp. 846-856
-
-
Karplus, K.1
Barrett, C.2
Hughey, R.3
-
16
-
-
0031743421
-
Profile Hidden Markov Models
-
10.1093/bioinformatics/14.9.755 9918945
-
Eddy S Profile Hidden Markov Models Bioinformatics 1998 14:755-763 10.1093/bioinformatics/14.9.755 9918945
-
(1998)
Bioinformatics
, vol.14
, pp. 755-763
-
-
Eddy, S.1
-
17
-
-
0021160693
-
The alignment of sets of sequences and the construction of phyletic trees: An integrated method
-
10.1007/BF02257378 6433036
-
Hogeweg P Hesper B The alignment of sets of sequences and the construction of phyletic trees: An integrated method J Mol Evol 1984 20(2):175-186 10.1007/BF02257378 6433036
-
(1984)
J Mol Evol
, vol.20
, Issue.2
, pp. 175-186
-
-
Hogeweg, P.1
Hesper, B.2
-
18
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
10.1007/BF02603120 3118049
-
Feng DF Doolittle RF Progressive sequence alignment as a prerequisite to correct phylogenetic trees J Mol Evol 1987 25:351-360 10.1007/BF02603120 3118049
-
(1987)
J Mol Evol
, vol.25
, pp. 351-360
-
-
Feng, D.F.1
Doolittle, R.F.2
-
19
-
-
23044471766
-
An algorithm for progressive multiple alignment of sequences with insertions
-
1180752 10.1073/pnas.0409137102
-
Löytynoja A Goldman N An algorithm for progressive multiple alignment of sequences with insertions PNAS 2005 102(30):10557-10562 1180752 16000407 10.1073/pnas.0409137102
-
(2005)
PNAS
, vol.102
, Issue.30
, pp. 10557-10562
-
-
Löytynoja, A.1
Goldman, N.2
-
20
-
-
0345457233
-
Using guide trees to construct multiple-sequence evolutionary HMMs
-
10.1093/bioinformatics/btg1019 12855451
-
Holmes I Using guide trees to construct multiple-sequence evolutionary HMMs Bioinformatics 2003 19:i147-i157 10.1093/bioinformatics/btg1019 12855451
-
(2003)
Bioinformatics
, vol.19
-
-
Holmes, I.1
-
21
-
-
36549075072
-
An Emerging Probabilistic Framework for Modeling Indels on Trees
-
10.1093/bioinformatics/btm402
-
Bradley R Holmes I An Emerging Probabilistic Framework for Modeling Indels on Trees Bioinformatics 2007 10.1093/bioinformatics/btm402 17804440
-
(2007)
Bioinformatics
-
-
Bradley, R.1
Holmes, I.2
-
22
-
-
17944382496
-
Assessing variability by joint sampling of alignments and mutation rates
-
10.1007/s002390010253 11677626
-
Metzler D Fleissner R von Haeseler A Wakolbinger A Assessing variability by joint sampling of alignments and mutation rates J Mol Evol 2001 53:660-669 10.1007/s002390010253 11677626
-
(2001)
J Mol Evol
, vol.53
, pp. 660-669
-
-
Metzler, D.1
Fleissner, R.2
von Haeseler, A.3
Wakolbinger, A.4
-
23
-
-
0034791551
-
Evolutionary HMMs: A Bayesian approach to multiple alignment
-
10.1093/bioinformatics/17.9.803 11590097
-
Holmes I Bruno W Evolutionary HMMs: A Bayesian approach to multiple alignment Bioinformatics 2001 17(9):803-820 10.1093/bioinformatics/ 17.9.803 11590097
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 803-820
-
-
Holmes, I.1
Bruno, W.2
-
25
-
-
25444443637
-
Bayesian Coestimation of Phylogeny and Sequence Alignment
-
1087833 15804354 10.1186/1471-2105-6-83
-
Lunter G Miklós I Drummond A Jensen J Hein J Bayesian Coestimation of Phylogeny and Sequence Alignment BMC Bioinformatics 2005 6:83 1087833 15804354 10.1186/1471-2105-6-83
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 83
-
-
Lunter, G.1
Miklós, I.2
Drummond, A.3
Jensen, J.4
Hein, J.5
-
26
-
-
25144452234
-
Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction
-
10.1080/10635150590950371 16085574
-
Fleissner R Metzler D von Haesaler A Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction Systematic Biology 2005 54:548-561 10.1080/10635150590950371 16085574
-
(2005)
Systematic Biology
, vol.54
, pp. 548-561
-
-
Fleissner, R.1
Metzler, D.2
von Haesaler, A.3
-
27
-
-
22844450838
-
Joint Bayesian estimation of alignment and phylogeny
-
10.1080/10635150590947041
-
Redelings B Suchard M Joint Bayesian estimation of alignment and phylogeny Syst Biol 2005 50:401-418 10.1080/10635150590947041
-
(2005)
Syst Biol
, vol.50
, pp. 401-418
-
-
Redelings, B.1
Suchard, M.2
-
28
-
-
33747863926
-
BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny
-
10.1093/bioinformatics/btl175 16679334
-
Suchard M Redelings B BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny Bioinformatics 2006 22(16):2047-2048 10.1093/ bioinformatics/btl175 16679334
-
(2006)
Bioinformatics
, vol.22
, pp. 2047-2048
-
-
Suchard, M.1
Redelings, B.2
-
30
-
-
77956890234
-
Monte Carlo sampling methods using Markov chains and their applications
-
10.1093/biomet/57.1.97
-
Hastings W Monte Carlo sampling methods using Markov chains and their applications Biometrica 1970 57:97-109 10.1093/biomet/57.1.97
-
(1970)
Biometrica
, vol.57
, pp. 97-109
-
-
Hastings, W.1
-
31
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
10.1093/bioinformatics/btg180 12912839
-
Ronquist F Huelsenbeck J MrBayes 3: Bayesian phylogenetic inference under mixed models Bioinformatics 2003 19(12):1572-1574 10.1093/ bioinformatics/btg180 12912839
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.2
-
34
-
-
0035749546
-
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement
-
Skolnick J Kolinski A Kihara D Betancourt M Rotkiewicz PMB M B Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement Proteins 2002 44(S5):149-156
-
(2002)
Proteins
, vol.44
, Issue.S5
, pp. 149-156
-
-
Skolnick, J.1
Kolinski, A.2
Kihara, D.3
Betancourt, M.4
Rotkiewicz, P.M.B.M.B.5
-
35
-
-
34249869832
-
Ab initio modeling of small proteins by iterative TASSER simulations
-
1878469 17488521 10.1186/1741-7007-5-17
-
Wu S Skolnick J Zhang Y Ab initio modeling of small proteins by iterative TASSER simulations BMC Biology 2007 5:17 1878469 17488521 10.1186/1741-7007-5-17
-
(2007)
BMC Biology
, vol.5
, pp. 17
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
36
-
-
34548608483
-
Ab Initio Protein Structure Prediction Using Chunk-TASSER
-
10.1529/biophysj.107.109959 17496016
-
Zhou H Skolnick J Ab Initio Protein Structure Prediction Using Chunk-TASSER Biophysical Journal 2007 93:1510-1518 10.1529/ biophysj.107.109959 17496016
-
(2007)
Biophysical Journal
, vol.93
, pp. 1510-1518
-
-
Zhou, H.1
Skolnick, J.2
-
37
-
-
0030601801
-
Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses
-
10.1006/jmbi.1996.0569 8913301
-
Goldman N Thorne J Jones D Using Evolutionary Trees in Protein Secondary Structure Prediction and Other Comparative Sequence Analyses J Mol Biol 1996 263(2):196-08 10.1006/jmbi.1996.0569 8913301
-
(1996)
J Mol Biol
, vol.263
, Issue.2
, pp. 196-208
-
-
Goldman, N.1
Thorne, J.2
Jones, D.3
-
38
-
-
0025334980
-
Improvements in Protein Secondary Structure Prediction by an Enhanced Neural Network
-
10.1016/0022-2836(90)90154-E 2370661
-
Kneller D Cohen F Langridge R Improvements in Protein Secondary Structure Prediction by an Enhanced Neural Network J Mol Biol 1990 214:171-182 10.1016/0022-2836(90)90154-E 2370661
-
(1990)
J Mol Biol
, vol.214
, pp. 171-182
-
-
Kneller, D.1
Cohen, F.2
Langridge, R.3
-
39
-
-
0029884694
-
GOR secondary structure prediction method version IV
-
8743705
-
Garnier J Gibrat JF B R GOR secondary structure prediction method version IV Methods in Enzymology 1996 266:540-553 8743705
-
(1996)
Methods in Enzymology
, vol.266
, pp. 540-553
-
-
Garnier, J.1
Gibrat, J.F.B.R.2
-
40
-
-
0031766401
-
HOMSTRAD: A database of protein structure alignments for homologous families
-
2143859 9828015
-
Mizuguchi K Deane CM Blundell TL P OJ HOMSTRAD: A database of protein structure alignments for homologous families Protein Science 1998 7:2469-2471 2143859 9828015
-
(1998)
Protein Science
, vol.7
, pp. 2469-2471
-
-
Mizuguchi, K.1
Deane, C.M.2
Blundell, T.L.P.O.J.3
-
41
-
-
0031714858
-
JOY: Protein sequence-structure representation and analysis
-
10.1093/bioinformatics/14.7.617 9730927
-
Mizuguchi K Deane C Johnson M Blundell T Overington J JOY: Protein sequence-structure representation and analysis Bioinformatics 1998 14:617-623 10.1093/bioinformatics/14.7.617 9730927
-
(1998)
Bioinformatics
, vol.14
, pp. 617-623
-
-
Mizuguchi, K.1
Deane, C.2
Johnson, M.3
Blundell, T.4
Overington, J.5
-
42
-
-
0000228203
-
-
National Biomedical Research Foundation, Washington, D.C., chap. A model of evolutionary changes in proteins
-
Dayhoff M Schwartz R Orcutt B Atlas of protein sequence and structure National Biomedical Research Foundation, Washington, D.C., chap. A model of evolutionary changes in proteins 1978 5:345-352
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 345-352
-
-
Dayhoff, M.1
Schwartz, R.2
Orcutt, B.3
-
43
-
-
0036298990
-
An expectation maximization algorithm for training hidden substitution models
-
10.1006/jmbi.2002.5405
-
Holmes I Rubin G An expectation maximization algorithm for training hidden substitution models J Mol Biol 2002 317:757-768 10.1006/ jmbi.2002.5405
-
(2002)
J Mol Biol
, vol.317
, pp. 757-768
-
-
Holmes, I.1
Rubin, G.2
-
45
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
10.1007/BF01734359
-
Felsenstein J Evolutionary trees from DNA sequences: A maximum likelihood approach J Mol Evol 1981 17:68-376 10.1007/BF01734359
-
(1981)
J Mol Evol
, vol.17
, pp. 68-376
-
-
Felsenstein, J.1
-
46
-
-
0036021407
-
Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data
-
1462188 12136032
-
Drummond A Nicholls G Rodrigo A Solomon W Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data Genetics 2002 161(3):1307-1320 1462188 12136032
-
(2002)
Genetics
, vol.161
, pp. 1307-1320
-
-
Drummond, A.1
Nicholls, G.2
Rodrigo, A.3
Solomon, W.4
-
47
-
-
0031721576
-
Dynamic programming alignment accuracy
-
Holmes I Durbin R Dynamic programming alignment accuracy J Comp Biol 1998 5:493-504
-
(1998)
J Comp Biol
, vol.5
, pp. 493-504
-
-
Holmes, I.1
Durbin, R.2
|