-
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):443-453. 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
-
-
0019764298
-
Comparative biosequence metrics
-
10.1007/BF01733210, 7334527
-
Smith TF, Waterman MS, Fitch WM. Comparative biosequence metrics. J Mol Evol 1981, 18(1):38-46. 10.1007/BF01733210, 7334527.
-
(1981)
J Mol Evol
, vol.18
, Issue.1
, pp. 38-46
-
-
Smith, T.F.1
Waterman, M.S.2
Fitch, W.M.3
-
3
-
-
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(4):351-360. 10.1007/BF02603120, 3118049.
-
(1987)
J Mol Evol
, vol.25
, Issue.4
, pp. 351-360
-
-
Feng, D.F.1
Doolittle, R.F.2
-
4
-
-
0027968068
-
CLUSTAL W: 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. Nucleic Acids Res 1994, 22(22):4673-4680. 10.1093/nar/22.22.4673, 308517, 7984417.
-
(1994)
Nucleic Acids Res
, vol.22
, Issue.22
, pp. 4673-4680
-
-
Thompson, J.D.1
Higgins, D.G.2
Gibson, T.J.3
-
5
-
-
45949105543
-
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment
-
10.1186/1748-7188-3-6, 2430965, 18505568
-
Subramanian AR, Kaufmann M, Morgenstern B. DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment. Algorithms Mol Biol 2008, 3:6. 10.1186/1748-7188-3-6, 2430965, 18505568.
-
(2008)
Algorithms Mol Biol
, vol.3
, pp. 6
-
-
Subramanian, A.R.1
Kaufmann, M.2
Morgenstern, B.3
-
6
-
-
0034623005
-
T-coffee: a novel method for fast and accurate multiple sequence alignment
-
10.1006/jmbi.2000.4042, 10964570
-
Notredame C, Higgins DG, Heringa J. T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302(1):205-217. 10.1006/jmbi.2000.4042, 10964570.
-
(2000)
J Mol Biol
, vol.302
, Issue.1
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
7
-
-
14644430471
-
ProbCons: probabilistic consistency-based multiple sequence alignment
-
10.1101/gr.2821705, 546535, 15687296
-
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15(2):330-340. 10.1101/gr.2821705, 546535, 15687296.
-
(2005)
Genome Res
, vol.15
, Issue.2
, pp. 330-340
-
-
Do, C.B.1
Mahabhashyam, M.S.2
Brudno, M.3
Batzoglou, S.4
-
8
-
-
33751004142
-
Probalign: multiple sequence alignment using partition function posterior probabilities
-
10.1093/bioinformatics/btl472, 16954142
-
Roshan U, Livesay DR. Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 2006, 22(22):2715-2721. 10.1093/bioinformatics/btl472, 16954142.
-
(2006)
Bioinformatics
, vol.22
, Issue.22
, pp. 2715-2721
-
-
Roshan, U.1
Livesay, D.R.2
-
9
-
-
80054078476
-
Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega
-
3261699, 21988835
-
Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol 2011, 7:539. 3261699, 21988835.
-
(2011)
Mol Syst Biol
, vol.7
, pp. 539
-
-
Sievers, F.1
Wilm, A.2
Dineen, D.3
Gibson, T.J.4
Karplus, K.5
Li, W.6
Lopez, R.7
McWilliam, H.8
Remmert, M.9
Söding, J.10
Thompson, J.D.11
Higgins, D.G.12
-
10
-
-
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):452-464. 10.1093/bioinformatics/18.3.452, 11934745.
-
(2002)
Bioinformatics
, vol.18
, Issue.3
, pp. 452-464
-
-
Lee, C.1
Grasso, C.2
Sharlow, M.F.3
-
11
-
-
0030582739
-
Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
-
10.1006/jmbi.1996.0679, 8980688
-
Gotoh O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 1996, 264(4):823-838. 10.1006/jmbi.1996.0679, 8980688.
-
(1996)
J Mol Biol
, vol.264
, Issue.4
, pp. 823-838
-
-
Gotoh, O.1
-
12
-
-
13244255415
-
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
-
Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinforma 2004, 5:113.
-
(2004)
BMC Bioinforma
, vol.5
, pp. 113
-
-
Edgar, R.C.1
-
13
-
-
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):3059-3066. 10.1093/nar/gkf436, 135756, 12136088.
-
(2002)
Nucleic Acids Res
, vol.30
, Issue.14
, pp. 3059-3066
-
-
Katoh, K.1
Misawa, K.2
Kuma, K.3
Miyata, T.4
-
14
-
-
0028928174
-
Comprehensive study on iterative algorithms of multiple sequence alignment
-
Hirosawa M, Totoki Y, Hoshida M, Ishikawa M. Comprehensive study on iterative algorithms of multiple sequence alignment. Comput Appl Biosci 1995, 11(1):13-18.
-
(1995)
Comput Appl Biosci
, vol.11
, Issue.1
, pp. 13-18
-
-
Hirosawa, M.1
Totoki, Y.2
Hoshida, M.3
Ishikawa, M.4
-
15
-
-
13744252890
-
MAFFT version 5: improvement in accuracy of multiple sequence alignment
-
10.1093/nar/gki198, 548345, 15661851
-
Katoh K, Kuma K, Toh H, Miyata T. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 2005, 33(2):511-518. 10.1093/nar/gki198, 548345, 15661851.
-
(2005)
Nucleic Acids Res
, vol.33
, Issue.2
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
-
16
-
-
24644457706
-
BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark
-
10.1002/prot.20527, 16044462
-
Thompson JD, Koehl P, Ripp R, Poch O. BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61(1):127-136. 10.1002/prot.20527, 16044462.
-
(2005)
Proteins
, vol.61
, Issue.1
, pp. 127-136
-
-
Thompson, J.D.1
Koehl, P.2
Ripp, R.3
Poch, O.4
-
17
-
-
0035175770
-
BAliBASE (benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations
-
10.1093/nar/29.1.323, 29792, 11125126
-
Bahr A, Thompson JD, Thierry JC, Poch O. BAliBASE (benchmark alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. Nucleic Acids Res 2001, 29(1):323-326. 10.1093/nar/29.1.323, 29792, 11125126.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 323-326
-
-
Bahr, A.1
Thompson, J.D.2
Thierry, J.C.3
Poch, O.4
-
18
-
-
43249091570
-
A new protein linear motif benchmark for multiple sequence alignment software
-
Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD. A new protein linear motif benchmark for multiple sequence alignment software. BMC Bioinforma 2008, 9:213.
-
(2008)
BMC Bioinforma
, vol.9
, pp. 213
-
-
Perrodou, E.1
Chica, C.2
Poch, O.3
Gibson, T.J.4
Thompson, J.D.5
-
19
-
-
0037010180
-
Quality assessment of multiple alignment programs
-
10.1016/S0014-5793(02)03189-7, 12354624
-
Lassmann T, Sonnhammer EL. Quality assessment of multiple alignment programs. FEBS Lett 2002, 529(1):126-130. 10.1016/S0014-5793(02)03189-7, 12354624.
-
(2002)
FEBS Lett
, vol.529
, Issue.1
, pp. 126-130
-
-
Lassmann, T.1
Sonnhammer, E.L.2
-
20
-
-
0033168097
-
A comprehensive comparison of multiple sequence alignment programs
-
10.1093/nar/27.13.2682, 148477, 10373585
-
Thompson JD, Plewniak F, Poch O. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 1999, 27(13):2682-2690. 10.1093/nar/27.13.2682, 148477, 10373585.
-
(1999)
Nucleic Acids Res
, vol.27
, Issue.13
, pp. 2682-2690
-
-
Thompson, J.D.1
Plewniak, F.2
Poch, O.3
-
21
-
-
33748940447
-
Analysis and comparison of benchmarks for multiple sequence alignment
-
Blackshields G, Wallace IM, Larkin M, Higgins DG. Analysis and comparison of benchmarks for multiple sequence alignment. In Silico Biol 2006, 6(4):321-339.
-
(2006)
In Silico Biol
, vol.6
, Issue.4
, pp. 321-339
-
-
Blackshields, G.1
Wallace, I.M.2
Larkin, M.3
Higgins, D.G.4
-
22
-
-
33750736013
-
The accuracy of several multiple sequence alignment programs for proteins
-
Nuin PA, Wang Z, Tillier ER. The accuracy of several multiple sequence alignment programs for proteins. BMC Bioinforma 2006, 7:471.
-
(2006)
BMC Bioinforma
, vol.7
, pp. 471
-
-
Nuin, P.A.1
Wang, Z.2
Tillier, E.R.3
-
23
-
-
0023984847
-
Optimal alignments in linear space
-
Myers EW, Miller W. Optimal alignments in linear space. Comput Appl Biosci 1988, 4(1):11-17.
-
(1988)
Comput Appl Biosci
, vol.4
, Issue.1
, pp. 11-17
-
-
Myers, E.W.1
Miller, W.2
-
24
-
-
72549111108
-
Optimizing substitution matrix choice and gap parameters for sequence alignment
-
Edgar RC. Optimizing substitution matrix choice and gap parameters for sequence alignment. BMC Bioinforma 2009, 10:396.
-
(2009)
BMC Bioinforma
, vol.10
, pp. 396
-
-
Edgar, R.C.1
-
25
-
-
45949107473
-
Recent developments in the MAFFT multiple sequence alignment program
-
10.1093/bib/bbn013, 18372315
-
Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 2008, 9(4):286-298. 10.1093/bib/bbn013, 18372315.
-
(2008)
Brief Bioinform
, vol.9
, Issue.4
, pp. 286-298
-
-
Katoh, K.1
Toh, H.2
-
26
-
-
77955019084
-
Parallelization of the MAFFT multiple sequence alignment program
-
10.1093/bioinformatics/btq224, 2905546, 20427515
-
Katoh K, Toh H. Parallelization of the MAFFT multiple sequence alignment program. Bioinformatics 2010, 26(15):1899-1900. 10.1093/bioinformatics/btq224, 2905546, 20427515.
-
(2010)
Bioinformatics
, vol.26
, Issue.15
, pp. 1899-1900
-
-
Katoh, K.1
Toh, H.2
-
27
-
-
77952039847
-
Sequence embedding for fast construction of guide trees for multiple sequence alignment
-
10.1186/1748-7188-5-21, 2893182, 20470396
-
Blackshields G, Sievers F, Shi W, Wilm A, Higgins DG. Sequence embedding for fast construction of guide trees for multiple sequence alignment. Algorithms Mol Biol 2010, 5:21. 10.1186/1748-7188-5-21, 2893182, 20470396.
-
(2010)
Algorithms Mol Biol
, vol.5
, pp. 21
-
-
Blackshields, G.1
Sievers, F.2
Shi, W.3
Wilm, A.4
Higgins, D.G.5
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