-
2
-
-
23044499051
-
Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics
-
Althaus,E. et al. (2002). Multiple sequence alignment with arbitrary gap costs: Computing an optimal solution using polyhedral combinatorics. In Proceedings of the 1st European Conference on Computational Biology (ECCB 2002), pp. 4-16.
-
(2002)
Proceedings of the 1st European Conference on Computational Biology (ECCB 2002)
, pp. 4-16
-
-
Althaus, E.1
-
3
-
-
29044432109
-
A branch-and-cut algorithm for multiple sequence alignment
-
Althaus,E. et al. (2006). A branch-and-cut algorithm for multiple sequence alignment. Math. Prog., 105, 387-425.
-
(2006)
Math. Prog
, vol.105
, pp. 387-425
-
-
Althaus, E.1
-
4
-
-
0025183708
-
Basic local alignment search tool
-
Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, pp. 403-410
-
-
Altschul, S.F.1
-
7
-
-
0033153375
-
Alignment of whole genomes
-
Delcher,A.L. et al. (1999) Alignment of whole genomes. Nucl. Acids. Res., 27, 2369-2376.
-
(1999)
Nucl. Acids. Res
, vol.27
, pp. 2369-2376
-
-
Delcher, A.L.1
-
8
-
-
49549116375
-
-
ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences, and, eds, AAAI Press/The MIT Press, pp
-
Chuong,B. et al. (2004) ProbCons: Probabilistic consistency-based multiple alignment of amino acid sequences. In Dcborah,L. McGuinness and George Ferguson, (eds), AAAI, AAAI Press/The MIT Press, pp. 703-708.
-
(2004)
AAAI
, pp. 703-708
-
-
Chuong, B.1
-
9
-
-
39549090389
-
SeqAn - an efficient, generic C++ library for sequence analysis
-
Döring,A. et al. (2008). SeqAn - an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9,11.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 11
-
-
Döring, A.1
-
11
-
-
3042666256
-
MUSCLE: Multiple sequence alignment with high accuracy and high throughput
-
Edgar,R.C. (2004) MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-17917.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1792-17917
-
-
Edgar, R.C.1
-
12
-
-
0023084055
-
Progressive sequence alignment as a prerequisite to correct phylogenetic trees
-
Feng,D.-F. and Doolittle,R.F. (1987) Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol., 25 351-360.
-
(1987)
J. Mol. Evol
, vol.25
, pp. 351-360
-
-
Feng, D.-F.1
Doolittle, R.F.2
-
13
-
-
0020484488
-
An improved algorithm for matching biological sequences
-
Gotoh,O. An improved algorithm for matching biological sequences. J. Mol. Biol., 162, 705-708.
-
J. Mol. Biol
, vol.162
, pp. 705-708
-
-
Gotoh, O.1
-
14
-
-
0025138774
-
Consistency of optimal sequence alignments
-
Gotoh,O. (1990) Consistency of optimal sequence alignments. BMB., 52.
-
(1990)
BMB
, vol.52
-
-
Gotoh, O.1
-
16
-
-
0016518550
-
A linear space algorithm for computing maximal common subsequences
-
Hirschberg,D.S. (1975) A linear space algorithm for computing maximal common subsequences. Commum. ACAY, 18. 341-343.
-
(1975)
Commum. ACAY
, vol.18
, pp. 341-343
-
-
Hirschberg, D.S.1
-
17
-
-
85005767936
-
Heaviest increasing/common subsequence problems
-
Springer-Verlag, London, UK, pp
-
Jacobson,G. and Vo,K.-P. (1992) Heaviest increasing/common subsequence problems. In Proceedings of the 3rd Annual Symposium on Combinatorial Pattern Matching (CPM). Springer-Verlag, London, UK, pp. 52-66.
-
(1992)
Proceedings of the 3rd Annual Symposium on Combinatorial Pattern Matching (CPM)
, pp. 52-66
-
-
Jacobson, G.1
Vo, K.-P.2
-
18
-
-
0037100671
-
MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
-
Katoh,K. et al (2002) MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 3059-3066
-
-
Katoh, K.1
-
20
-
-
0032892093
-
An exact solution for the segment-to-segment multiple sequence alignment problem
-
Lenhof,H.-P. et al. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. Bioinformatics, 15, 203-210.
-
(1999)
Bioinformatics
, vol.15
, pp. 203-210
-
-
Lenhof, H.-P.1
-
21
-
-
0034352262
-
The practical use of the A* algorithm for exact multiple sequence alignment
-
Lermen,M. and Reinert,K. (2000) The practical use of the A* algorithm for exact multiple sequence alignment. J. Comp. Biol., 7, 655-671.
-
(2000)
J. Comp. Biol
, vol.7
, pp. 655-671
-
-
Lermen, M.1
Reinert, K.2
-
22
-
-
0009620624
-
A tool for multiple sequence alignment
-
Lipman,D.J. et al. (1989) A tool for multiple sequence alignment. Proc. Natl Acad. Sci. USA, 86, 4412-4415.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 4412-4415
-
-
Lipman, D.J.1
-
23
-
-
84967416712
-
Chaining multiple-alignment fragments in sub-quadratic fime
-
Society for Industrial and Applied Mathematics, San Francisco, California, pp
-
Myers,G. and Miller,W. (1995) Chaining multiple-alignment fragments in sub-quadratic fime. In Proceedings of 6th Annual SODA: ACM-SIAM Symposium on Discrete Algorithms (A Conference on Theoretical and Experimetal Analysis of Discrete Algorithms). Society for Industrial and Applied Mathematics, San Francisco, California, pp. 38-47.
-
(1995)
Proceedings of 6th Annual SODA: ACM-SIAM Symposium on Discrete Algorithms (A Conference on Theoretical and Experimetal Analysis of Discrete Algorithms)
, pp. 38-47
-
-
Myers, G.1
Miller, W.2
-
24
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman,S.B. and Wunsch,C.D. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Molecular Biol., 48, 443-453.
-
(1970)
J. Molecular Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.B.1
Wunsch, C.D.2
-
25
-
-
0034623005
-
T-Coffee: A novel method for fast and accurate multiple sequence alignment
-
Notredame,C. et al. (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
-
26
-
-
33750001271
-
MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information
-
Pei,J. and Grishin,N.V. (2007) MUMMALS: Multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic Acids Res., 34, 4364-4374.
-
(2007)
Nucleic Acids Res
, vol.34
, pp. 4364-4374
-
-
Pei, J.1
Grishin, N.V.2
-
27
-
-
34248532415
-
PROMALS: Towards accurate multiple sequence alignments of distantly related proteins
-
Pei,J. and Grishin,N.V. (2006) PROMALS: Towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics, 23, 802-808.
-
(2006)
Bioinformatics
, vol.23
, pp. 802-808
-
-
Pei, J.1
Grishin, N.V.2
-
28
-
-
0033665509
-
An iterative methods for faster sum-of-pairs multiple sequence alignment
-
Reinert,K. et al. (2000) An iterative methods for faster sum-of-pairs multiple sequence alignment. Bioinformatics, 16 808-814.
-
(2000)
Bioinformatics
, vol.16
, pp. 808-814
-
-
Reinert, K.1
-
29
-
-
0023375195
-
The neighbor-joining method: A new method for reconstructing phylogenetic trees
-
Saitou,N. and 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
-
-
0003725141
-
-
Addison-Wesley, Reading, MA
-
Sankoff,A. and Kruskal,J. (1983) Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley, Reading, MA.
-
(1983)
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
-
-
Sankoff, A.1
Kruskal, J.2
-
31
-
-
33846659941
-
Multiple alignment by sequence annealing
-
Schwartz,A.S. and Pachter,L. (2007) Multiple alignment by sequence annealing. Bioinformatics, 23, e24-e29.
-
(2007)
Bioinformatics
, vol.23
-
-
Schwartz, A.S.1
Pachter, L.2
-
32
-
-
0000825481
-
A statistical method for evaluating systematic relationships
-
Sokal,R.R. and Michener,C.D. (1958) A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull., 38, 1409-1438.
-
(1958)
Univ. Kansas Sci. Bull
, vol.38
, pp. 1409-1438
-
-
Sokal, R.R.1
Michener, C.D.2
-
33
-
-
20444489707
-
DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
-
Subramanian,A.R. et al. (2005) DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics, 6, 66.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 66
-
-
Subramanian, A.R.1
-
34
-
-
33745632116
-
AuberGene-a sensitive genome alignment tool
-
Szklarczyk,R. and Heringa,J. (2006) AuberGene-a sensitive genome alignment tool. Bioinformatics, 22, 1431-1436.
-
(2006)
Bioinformatics
, vol.22
, pp. 1431-1436
-
-
Szklarczyk, R.1
Heringa, J.2
-
35
-
-
0027968068
-
-
Thompson.J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
Thompson.J.D. et al. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
-
-
-
-
36
-
-
24644457706
-
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark
-
Thompson,J.D. et al. (2005) BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins, 61, 127-136.
-
(2005)
Proteins
, vol.61
, pp. 127-136
-
-
Thompson, J.D.1
-
37
-
-
0032988850
-
BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
-
Thompson,J.D. et al. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
-
(1999)
Bioinformatics
, vol.15
, pp. 87-88
-
-
Thompson, J.D.1
-
38
-
-
33645507429
-
M-Coffee: Combining multiple sequence alignment methods with T-Coffee
-
Wallace,I.M. et al. (2006) M-Coffee: Combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1692-1699
-
-
Wallace, I.M.1
-
39
-
-
0028679709
-
On the complexity of multiple sequence alignment
-
Wang,L. and Jiang,T. (1994) On the complexity of multiple sequence alignment. J. Comput. Biol., 1, 337-348.
-
(1994)
J. Comput. Biol
, vol.1
, pp. 337-348
-
-
Wang, L.1
Jiang, T.2
-
40
-
-
0023661088
-
-
Waterman,M.S. and Eggert.M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol 197, 723-728
-
Waterman,M.S. and Eggert.M. (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol 197, 723-728
-
-
-
-
41
-
-
34547840223
-
Multiple alignment by aligning alignments
-
Wheeler,T.J. and Kececioglu,J.D. (2007) Multiple alignment by aligning alignments. Bioinformatics, 23, 559-568.
-
(2007)
Bioinformatics
, vol.23
, pp. 559-568
-
-
Wheeler, T.J.1
Kececioglu, J.D.2
|