-
1
-
-
80052262050
-
Finding the balance between the mathematical and biological optima in multiple sequence alignment
-
Anisimova M, Cannarozzi G, Liberles DA. Finding the balance between the mathematical and biological optima in multiple sequence alignment. Trends in Evolutionary Biol 2010, 2:e7. [http://www.pagepress.org/journals/index.php/eb/article/view/ eb.2010.e7/2536].
-
(2010)
Trends in Evolutionary Biol
, vol.2
-
-
Anisimova, M.1
Cannarozzi, G.2
Liberles, D.A.3
-
2
-
-
0036203448
-
Multiple sequence alignment using partial order graphs
-
10.1093/bioinformatics/18.3.452, 11934745
-
Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452. [http://bioinformatics.oxfordjournals.org/content/18/3/452.ab stract], 10.1093/bioinformatics/18.3.452, 11934745.
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 452
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
3
-
-
23044471766
-
An algorithm for progressive multiple alignment of sequences with insertions
-
Löytynoja A, Goldman N. An algorithm for progressive multiple alignment of sequences with insertions. Proc National Acad Sci USA 2005, 102(30):10557. [http://www.pnas.org/content/102/30/10557.abstract].
-
(2005)
Proc National Acad Sci USA
, vol.102
, Issue.30
, pp. 10557
-
-
Löytynoja, A.1
Goldman, N.2
-
4
-
-
84864006216
-
Accurate Extension of Multiple Sequence Alignments Using a Phylogeny-Aware Graph Algorithm
-
Löytynoja A, Vilella AJ, Goldman N. Accurate Extension of Multiple Sequence Alignments Using a Phylogeny-Aware Graph Algorithm. Bioinformatics 2012, [http://bioinformatics.oxfordjournals.org/content/early/2012/04/23/bioin formatics.bts198].
-
(2012)
Bioinformatics
-
-
Löytynoja, A.1
Vilella, A.J.2
Goldman, N.3
-
5
-
-
0030807655
-
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data
-
10.1093/oxfordjournals.molbev.a025808, 9254330
-
Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997, 14(7):685. [http://mbe.oxfordjournals.org/content/14/7/685.abstract], 10.1093/oxfordjournals.molbev.a025808, 9254330.
-
(1997)
Mol Biol Evol
, vol.14
, Issue.7
, pp. 685
-
-
Gascuel, O.1
-
6
-
-
0036166508
-
Integrated gene and species phylogenies from unaligned whole genome protein sequences
-
10.1093/bioinformatics/18.1.100, 11836217
-
Stuart GW, Moffett K, Baker S. Integrated gene and species phylogenies from unaligned whole genome protein sequences. Bioinformatics 2002, 18:100. [http://bioinformatics.oxfordjournals.org/content/18/1/100.abstract], 10.1093/bioinformatics/18.1.100, 11836217.
-
(2002)
Bioinformatics
, vol.18
, pp. 100
-
-
Stuart, G.W.1
Moffett, K.2
Baker, S.3
-
7
-
-
0029985399
-
Combining protein evolution and secondary structure
-
10.1093/oxfordjournals.molbev.a025627, 8676741
-
Thorne JL, Goldman N, Jones DT. Combining protein evolution and secondary structure. Mol Biol Evol 1996, 13(5):666. [http://mbe.oxfordjournals.org/content/13/5/666.abstract], 10.1093/oxfordjournals.molbev.a025627, 8676741.
-
(1996)
Mol Biol Evol
, vol.13
, Issue.5
, pp. 666
-
-
Thorne, J.L.1
Goldman, N.2
Jones, D.T.3
-
8
-
-
79957599007
-
Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions
-
10.1371/journal.pone.0020488, 3103576, 21647374
-
Szalkowski AM, Anisimova M. Markov Models of Amino Acid Substitution to Study Proteins with Intrinsically Disordered Regions. PLoS ONE 2011, 6(5):e20488. [http://dx.doi.org/10.1371], 10.1371/journal.pone.0020488, 3103576, 21647374.
-
(2011)
PLoS ONE
, vol.6
, Issue.5
-
-
Szalkowski, A.M.1
Anisimova, M.2
-
9
-
-
62649147821
-
Sequence context-specific profiles for homology searching
-
Biegert A, Söding J. Sequence context-specific profiles for homology searching. Proc National Acad Sci 2009, 106(10):3770. [http://www.pnas.org/content/106/10/3770.abstract].
-
(2009)
Proc National Acad Sci
, vol.106
, Issue.10
, pp. 3770
-
-
Biegert, A.1
Söding, J.2
-
10
-
-
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. [http://www.sciencedirect.com/science/article/pii/0022283670900574], 10.1016/0022-2836(70)90057-4, 5420325.
-
(1970)
J Mol Biol
, vol.48
, Issue.3
, pp. 443
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
11
-
-
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(3):705. [http://www.sciencedirect.com/science/article/pii/0022283682903989], 10.1016/0022-2836(82)90398-9, 7166760.
-
(1982)
J Mol Biol
, vol.162
, Issue.3
, pp. 705
-
-
Gotoh, O.1
-
12
-
-
84935113569
-
Error bounds for convolutional codes and an asymptotically optimum decoding algorithm
-
Viterbi A. Error bounds for convolutional codes and an asymptotically optimum decoding algorithm. Inf Theory, IEEE Trans 1967, 13(2):260.
-
(1967)
Inf Theory, IEEE Trans
, vol.13
, Issue.2
, pp. 260
-
-
Viterbi, A.1
-
13
-
-
55549095155
-
Genome-wide nucleotide-level mammalian ancestor reconstruction
-
10.1101/gr.076521.108, 2577868, 18849525
-
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res 2008, 18(11):1829. [http://genome.cshlp.org/content/18/11/1829.abstract], 10.1101/gr.076521.108, 2577868, 18849525.
-
(2008)
Genome Res
, vol.18
, Issue.11
, pp. 1829
-
-
Paten, B.1
Herrero, J.2
Fitzgerald, S.3
Beal, K.4
Flicek, P.5
Holmes, I.6
Birney, E.7
-
14
-
-
3543097981
-
Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems
-
10.1093/bioinformatics/bth126, 14962922
-
Grasso C, Lee C. Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 2004, 20(10):1546. [http://bioinformatics.oxfordjournals.org/content/20/10/1546.abstract], 10.1093/bioinformatics/bth126, 14962922.
-
(2004)
Bioinformatics
, vol.20
, Issue.10
, pp. 1546
-
-
Grasso, C.1
Lee, C.2
-
15
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins: Struct, Funct, Bioinf 2005, 61:127. [http://onlinelibrary.wiley.com/doi/10.1002/prot.20527/full].
-
(2005)
Proteins: Struct, Funct, Bioinf
, vol.61
, pp. 127
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
16
-
-
0034073452
-
Darwin v. 2.0: an interpreted computer language for the biosciences
-
10.1093/bioinformatics/16.2.101, 10842729
-
Gonnet GH, Hallett MT, Korostensky C, Bernardin L. Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics 2000, 16(2):101. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/16/2/101] , 10.1093/bioinformatics/16.2.101, 10842729.
-
(2000)
Bioinformatics
, vol.16
, Issue.2
, pp. 101
-
-
Gonnet, G.H.1
Hallett, M.T.2
Korostensky, C.3
Bernardin, L.4
-
17
-
-
0027483434
-
Empirical and Structural Models for Insertions and Deletions in the Divergent Evolution of Proteins
-
10.1006/jmbi.1993.1105, 8445636
-
Benner SA, Cohen MA, Gonnet GH. Empirical and Structural Models for Insertions and Deletions in the Divergent Evolution of Proteins. J Mol Biol 1993, 229(4):1065. [http://www.sciencedirect.com/science/article/pii/S0022283683711058], 10.1006/jmbi.1993.1105, 8445636.
-
(1993)
J Mol Biol
, vol.229
, Issue.4
, pp. 1065
-
-
Benner, S.A.1
Cohen, M.A.2
Gonnet, G.H.3
-
18
-
-
0026566796
-
Analysis of insertions/deletions in protein structures
-
10.1016/0022-2836(92)91008-D, 1560462
-
Pascarella S, Argos P. Analysis of insertions/deletions in protein structures. J Mol Biol 1992, 224(2):461. [http://www.sciencedirect.com/science/article/pii/002228369291008D], 10.1016/0022-2836(92)91008-D, 1560462.
-
(1992)
J Mol Biol
, vol.224
, Issue.2
, pp. 461
-
-
Pascarella, S.1
Argos, P.2
-
20
-
-
84869100453
-
Probabilistic ancestral sequences and multiple alignments
-
[doi: 10.1007/3-540-61422-2_147]
-
Gonnet GH, Benner SA. Probabilistic ancestral sequences and multiple alignments. Algorithm Theory-SWAT'96 1996, 1097/1996:380. [doi: 10.1007/3-540-61422-2_147].
-
(1996)
Algorithm Theory-SWAT'96
, vol.1097
, pp. 380
-
-
Gonnet, G.H.1
Benner, S.A.2
-
21
-
-
0026656815
-
Exhaustive matching of the entire protein sequence database
-
10.1126/science.1604319, 1604319
-
Gonnet G, Cohen M, Benner S. Exhaustive matching of the entire protein sequence database. Science 1992, 256(5062):1443. [http://www.sciencemag.org/content/256/5062/1443.abstract], 10.1126/science.1604319, 1604319.
-
(1992)
Science
, vol.256
, Issue.5062
, pp. 1443
-
-
Gonnet, G.1
Cohen, M.2
Benner, S.3
-
22
-
-
0035031966
-
A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
-
10.1093/oxfordjournals.molbev.a003851, 11319253
-
Whelan S, Goldman N. A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach. Mol Biol Evol 2001, 18(5):691. [http://mbe.oxfordjournals.org/cgi/content/abstract/18/5/691], 10.1093/oxfordjournals.molbev.a003851, 11319253.
-
(2001)
Mol Biol Evol
, vol.18
, Issue.5
, pp. 691
-
-
Whelan, S.1
Goldman, N.2
-
23
-
-
0019797407
-
Evolutionary trees from DNA sequences: A maximum likelihood approach
-
10.1007/BF01734359, 7288891
-
Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981, 17(6):368. [http://www.springerlink.com/content/g2202t346n826461/], 10.1007/BF01734359, 7288891.
-
(1981)
J Mol Evol
, vol.17
, Issue.6
, pp. 368
-
-
Felsenstein, J.1
-
24
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
10.1093/nar/gkh340, 390337, 15034147
-
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004, 32(5):1792. [http://www.nar.oupjournals.org/cgi/doi/10.1093/nar/gkh340], 10.1093/nar/gkh340, 390337, 15034147.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.5
, pp. 1792
-
-
Edgar, R.C.1
-
25
-
-
84869112730
-
-
Cambridge, UK: Cambridge University Press
-
Kimura M. Neutral Theory Mol Evol 1985, Cambridge, UK: Cambridge University Press.
-
(1985)
Neutral Theory Mol Evol
-
-
Kimura, M.1
-
26
-
-
0037100671
-
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
-
10.1093/nar/gkf436, 135756, 12136088
-
Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002, 30(14):3059. 10.1093/nar/gkf436, 135756, 12136088.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.14
, pp. 3059
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
27
-
-
0027968068
-
Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
10.1093/nar/22.22.4673, 308517, 7984417
-
Thompson JD, Higgins DG, Gibson TJ, Clustal W. Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994, 22(22):4673. [http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673], 10.1093/nar/22.22.4673, 308517, 7984417.
-
(1994)
Nucl Acids Res
, vol.22
, Issue.22
, pp. 4673
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
Clustal, W.4
-
28
-
-
77950538424
-
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
-
10.1186/gb-2010-11-4-r37, 2884540, 20370897
-
Dessimoz C, Gil M. Phylogenetic assessment of alignments reveals neglected tree signal in gaps. Genome Biol 2010, 11(4):R37. [http://genomebiology.com/2010/11/4/R37/abstract], 10.1186/gb-2010-11-4-r37, 2884540, 20370897.
-
(2010)
Genome Biol
, vol.11
, Issue.4
-
-
Dessimoz, C.1
Gil, M.2
-
30
-
-
0034237578
-
Largescale comparison of protein sequence alignment algorithms with structure alignments
-
Sauder JM, Arthur JW, Dunbrack RL. Largescale comparison of protein sequence alignment algorithms with structure alignments. Proteins: Struct, Func, Bioinf 2000, 40:6. [http://onlinelibrary.wiley.com/doi/10.1002/(SICI)1097-0134(20000701)40: 16::AID-PROT303.0.CO;2-7/abstract].
-
(2000)
Proteins: Struct, Func, Bioinf
, vol.40
, pp. 6
-
-
Sauder, J.M.1
Arthur, J.W.2
Dunbrack, R.L.3
-
31
-
-
46249095233
-
Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
-
10.1126/science.1158395, 18566285
-
Löytynoja A, Goldman N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis. Science 2008, 320(5883):1632. 10.1126/science.1158395, 18566285.
-
(2008)
Science
, vol.320
, Issue.5883
, pp. 1632
-
-
Löytynoja, A.1
Goldman, N.2
-
32
-
-
78651316211
-
OMA 2011: orthology inference among 1000 complete genomes
-
Altenhoff AM, Schneider A, Gonnet GH, Dessimoz C. OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res 2010, 39(Database):1632. [http://nar.oxfordjournals.org/content/39/suppl_1/D289.short].
-
(2010)
Nucleic Acids Res
, vol.39
, Issue.DATABASE
, pp. 1632
-
-
Altenhoff, A.M.1
Schneider, A.2
Gonnet, G.H.3
Dessimoz, C.4
-
33
-
-
0019424782
-
Comparison of phylogenetic trees
-
Robinson D, Foulds L. Comparison of phylogenetic trees. Math Biosci 1981, 53(1-2):131. [http://www.sciencedirect.com/science/article/pii/0025556481900432].
-
(1981)
Math Biosci
, vol.53
, Issue.1-2
, pp. 131
-
-
Robinson, D.1
Foulds, L.2
|