References:
• Ewan Birney, Michele Clamp, and Richard Durbin (2004)
  GeneWise and Genomewise
  Genome Res. 14: 988-995
  Pairwise sequence comparison (Wise)

• Nicolas Bray and Lior Pachter
  MAVID: constrained ancestral alignment of multiple sequences
  Genome Res. 14: 693-699
  Multiple genome comparison (MAVID)

• Steven E. Brenner, Cyrus Chothia, and Tim J.P. Hubbard (1998)
  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
  Proc. Natl. Acad. Sci. USA 95: 6073-6078
  Comparison of algorithms for pairwise sequence comparisons

• Nigel P. Brown, Christophe Leroy, and Chris Sander (1998)
  MView: a web-compatible database search or multiple alignment viewer
  Bioinformatics 14: 380-381
  Representation of a multiple sequence alignment (MView)

• Michael Brudno, Michael Chapman, Berthold Göttgens, Serafim Batzoglou, and Burkhard Morgenstern (2003)
  Fast and sensitive multiple alignment of large genomic sequences
  BMC Bioinformatics 4: 66
  Multiple genome comparison (DIALIGN/CHAOS)

• Michael Brudno, Chuong B. Do, Gregory M. Cooper, Michael F. Kim, Eugene Davydov, Eric D. RED, Arend Sidow, Serafim Batzoglou, and NISC Comparative Sequencing Program (2003)
  LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
  Genome Res. 13: 721-731
  Multiple genome comparison (LAGAN/Multi-LAGAN)

• Klaus Bucka-Lassen, Ole Caprani, and Jotun Hein (1999)
  Combining many multiple alignments in one improved alignment
  Bioinformatics 15: 122-130
  Comparison of algorithms for multiple sequence comparisons

• Florence Corpet (1988)
  Multiple sequence alignment with hierarchical clustering
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  Multiple sequence comparison (Multalin)

• Jean-Michel Claverie (1993)
  Detecting frame shifts by amino acid sequence comparison
  J. Mol. Biol. 234: 1140-1157
  Original similarity matrix

• M.O. Dayhoff, R.M. Schwartz, and B.C. Orcutt (1978)
  A model of evolutionary change in proteins
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  Original similarity matrix

• Chuong B. Do, Mahathi S.P. Mahabhashyam, Michael Brudno, and Serafim Batzoglou (2005)
  ProbCons: Probabilistic consistency-based multiple sequence alignment
  Genome Res. 15: 330-340
  Multiple sequence comparison (ProbCons)

• D. Donnelly, J.P. Overington, S.V. Ruffle, J.H. Nugent, and T.L. Blundell (1993)
  Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues
  Protein Sci. 2: 55-70
  Original similarity matrix

• L. Duret, E. Gasteiger and G. Perrière (1996)
  LalnView: a graphical viewer for pairwise sequence alignments
  Comput. Applic. Biosci. 12: 507-510
  Representation of a parwise sequence alignment (LalnView)

• Robert C. Edgar (2004)
  MUSCLE: multiple sequence alignment with high accuracy and high throughput
  Nucleic Acids Res. 32: 1792-1797
  Multiple sequence comparison (MUSCLE)

• Robert C. Edgar (2004)
  MUSCLE: a multiple sequence alignment method with reduced time and space complexity
  BMC Bioinformatics 5: 113
  Multiple sequence comparison (MUSCLE)

• Robert C. Edgar and Kimmen Sjølander (2003)
  SATCHMO: sequence alignment and tree construction using hidden Markov models
  Bioinformatics 19: 1404-1411
  Multiple sequence comparison (SATCHMO)

• Robert C. Edgar and Kimmen Sjølander (2004)
  A comparison of scoring functions for protein sequence profile alignment
  Bioinformatics 20: 1301-1308
  Multiple profile-profile sequence comparison

• Robert C. Edgar and Kimmen Sjølander (2004)
  COACH: profile-profile alignment of protein families using hidden Markov models
  Bioinformatics 20: 1309-1318
  Multiple profile-profile sequence comparison (COACH)

• Arne Elofsson (2002)
  A study on protein sequence alignment quality
  Proteins 46: 330-339
  Comparison of algorithms for pairwise sequence comparisons
  Comparison of algorithms for multiple sequence comparisons

• Liliana Florea, George Hartzell, Zheng Zhang, Gerald M. Rubin, and Webb Miller (1998)
  A computer program for aligning a cDNA sequence with a genomic DNA sequence
  Genome Res. 8: 967-974
  Pairwise sequence comparison (SIM4)

• G.H. Gonnet, C. Korostensky, and S. Benner (2000)
  Evaluation measures of multiple sequence alignments
  J. Comput. Biol. 7: 261-276
  Comparison of algorithms for multiple sequence comparisons

• Steven Henikoff and Jorja G. Henikoff (1992)
  Amino acid substitution matrices from protein blocks
  Proc. Natl. Acad. Sci. USA 89: 10915-10919
  Original similarity matrix

• Steven Henikoff and Jorja G. Henikoff (1993)
  Performance evaluation of amino acid substitution matrices
  Proteins Struct. Funct. Genet. 17: 49-61
  Comparison of similarity matrices

• Steven Henikoff and Jorja G. Henikoff (2000)
  Amino acid substitution matrices
  Adv. Protein Chem. 54: 73-97
  Comparison of similarity matrices

• Desmond G. Higgins and Paul M. Sharp (1988)
  CLUSTAL: a package for performing multiple sequence alignment on a microcomputer
  Gene 73: 237-244
  Multiple sequence comparison (Clustal)

• D.G. Higgins, A.J. Bleasby, and R. Fuchs (1992)
  CLUSTAL V: improved software for multiple sequence alignment
  Comput. Appl. Biosci. 8: 189-191
  Multiple sequence comparison (Clustal)

• D.G. Higgins, J.D. Thompson, and T.J. Gibson (1996)
  Using CLUSTAL for multiple sequence alignments
  Methods Enzymol. 266: 383-402
  Multiple sequence comparison (Clustal)

• Xiaoquin Huang and Webb Miller (1991)
  A time-efficient, linear-space local similarity algorithm
  Adv. Appl. Mathemat. 12: 337-357
  Pairwise sequence comparison

• Lukasz Jaroszewski, Leszek Rychlewski, and Adam Godzik (2000)
  Improving the quality of twilight-zone alignments
  Protein Sci. 9: 1487-1496
  Multiple profile-profile sequence comparison (FFAS03)

• Lukasz Jaroszewski, Leszek Rychlewski, Zhanwen Li, Weizhong Li, and Adam Godzik (2005)
  FFAS03: a server for profile—profile sequence alignments
  Nucleic Acids Res. 33: W284-W288
  Multiple profile-profile sequence comparison (FFAS03)

• Francois Jeanmougin, Julie D. Thompson, Manolo Gouy, Desmond G. Higgins, and Toby J. Gibson (1988)
  Multiple sequence alignment with Clustal X.
  Trends Biochem. Sci. 23: 403-405
  Multiple sequence comparison (Clustal)

• Mark S. Johnson and John P. Overington (1993)
  A structural basis for sequence comparisons. An evaluation of scoring methodologies
  J. Mol. Biol. 233: 716-738
  Original similarity matrix
  Comparison of similarity matrices

• Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, and Takashi Miyata (2005)
  MAFFT version 5: improvement in accuracy of multiple sequence alignment
  Nucleic Acids Res. 33: 511-518
  Multiple sequence comparison (MAFFT)

• Kazutaka Katoh, Kazuhara Misawa, Kei-ichi Kuma, and Takashi Miyata (2002)
  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
  Nucleic Acids Res. 30: 3059-3066
  Multiple sequence comparison (MAFFT)

• Jeffrey M. Koshi and Richard A. Goldstein (1997)
  Mutation matrices and physical-chemical properties: correlations and implications
  Proteins Struct. Funct. Genet. 27: 336-344
  Comparison of similarity matrices

• Timo Lassmann and Eric L. Sonnhammer (2002)
  Quality assessment of multiple alignment programs
  FEBS Lett. 529: 126-130
  Comparison of algorithms for multiple sequence comparisons

• Odile Lecompte, Julie D. Thompson, Frédéric Plewniak, Jean-Claude Thierry, and Olivier Poch (2001)
  Multiple alignment of complete sequences (MACS) in the post-genomic era
  Gene 270:17-30
  Comparison of algorithms for multiple sequence comparisons

• David J. Lipman, Stephen F. Altschul, and John D. Kececioglu (1989)
  A tool for multiple sequence alignment
  Proc. Natl. Acad. Sci. USA 86: 4412-4415
  Multiple sequence comparison

• C.D. Livingstone and G.J. Barton (1993)
  Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation
  Comput. Appl. Biosci.9: 745-756
  Representation of a multiple sequence alignment (AMAS)

• Martin Madera and Julian Gough (2002)
  A comparison of profile hidden Markov model procedures for remote homology detection
  Nucleic Acids Res. 30: 4321-4328
  Multiple profile-profile sequence comparison

• Marc A. Marti-Renom, M.S. Madhusudhan, and Andrej Sali (2004)
  Alignment of protein sequences by their profiles
  Protein Sci. 13: 1071-1087
  Multiple profile-profile sequence comparison

• Alex C. May (1999)
  Towards more meaningful hierarchical classification of amino acid scoring matrices
  Protein Eng. 12: 707-712
  Comparison of similarity matrices

• Marcella A. McClure, Taha K. Vasi, and Walter M. Fitch (1994)
  Comparative analysis of multiple protein-sequence alignment methods
  Mol. Biol. Evol. 11: 571-592
  Comparison of algorithms for multiple sequence comparisons

• Burkhard Morgenstern (2000)
  A space-efficient algorithm for aligning large genomic sequences
  Bioinformatics 16: 948-949
  Pairwise sequence comparison (DIALIGN)

• Burkhard Morgenstern, Andreas Dress, and Thomas Werner (1996)
  Multiple DNA and protein sequence alignment based on segment-to-segment comparison
  Proc. Natl. Acad. Sci. USA 93: 12098-12103
  Multiple sequence comparison (DIALIGN)

• Burkhard Morgenstern, Kornelie Frech, Andreas Dress, and Thomas Werner (1998)
  DIALIGN: finding local similarities by multiple sequence alignment
  Bioinformatics 14: 290-294
  Multiple sequence comparison (DIALIGN)

• Burkhard Morgenstern (1999)
  DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment
  Bioinformatics 15: 211-218
  Multiple sequence comparison (DIALIGN)

• Saul B. Needleman and Christian D. Wunsch (1970)
  A general method applicable to the search for similarities in the amino acid sequence of two proteins
  J. Mol. Biol. 48: 443-453
  Pairwise sequence comparison

• Pauline C. Ng, Jorja G. Henikoff, and Steven Henikoff (2000)
  PHAT: a transmembrane-specific substitution matrix. predicted hydrophobic and transmembrane
  Bioinformatics 16: 760-766
  Original similarity matrix

• Pierre Nicodème (1998)
  SSMAL: similarity searching with alignment graphs
  Bioinformatics 14: 508-515
  Multiple sequence comparison (SSMAL)

• Cédric Notredame and Desmond G. Higgins (1996)
  SAGA: sequence alignment by genetic algorithm
  Nucleic Acids Res. 24: 1515-1524
  Multiple sequence comparison (SAGA)

• Cédric Notredame, Liisa Holm, and Desmond G. Higgins (1998)
  COFFEE: an objective function for multiple sequence alignments
  Bioinformatics 14: 407-422
  Comparison of algorithms for multiple sequence comparisons

• Cédric Notredame, Desmond G. Higgins, and J. Heringa (2000)
  T-Coffee: A novel method for fast and accurate multiple sequence alignment
  J. Mol. Biol. 302: 205-217
  Multiple sequence comparison (T-Coffee)

• Cédric Notredame (2001)
  Mocca: semi-automatic method for domain hunting
  Bioinformatics 17: 373-374
  Multiple sequence comparison / Repeats (Mocca)

• Tomas Ohlson, Björn Wallner, and Arne Elofsson (2004)
  Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods
  Proteins 57: 188-197
  Multiple profile-profile sequence comparison

• Orla O'Sullivan, Karsten Suhre, Chantal Abergel, Desmond G. Higgins, and Cédric Notredame (2004)
  3DCoffee: combining protein sequences and structures within multiple sequence alignments
  J. Mol. Biol. 340: 385-395
  Multiple sequence comparison (3DCoffee)

• L. Parida, A. Floratos and I. Rigoutsos (1998)
  MUSCA: an algorithm for constrained alignment of multiple data sequences
  Genome Inform. Ser. Workshop Genome Inform. 9: 112-119
  Multiple sequence comparison (MUSCA)

• L. Parida, A. Floratos and I. Rigoutsos (1999)
  An approximation algorithm for alignment of multiple sequences using motif discovery
  J. Combinat. Optimizat. 3: 247-275
  Multiple sequence comparison (MUSCA)

• William R. Pearson (1995)
  Comparison of methods for searching protein sequence databases
  Protein Sci. 4: 1145-1160
  Comparison of similarity matrices

• Nicholas J. Dickens and Chris P. Ponting (2003)
  THoR: a tool for domain discovery and curation of multiple alignments
  Genome Biol. 4: R52
  Representation of a multiple sequence alignment (THoR)

• Andreas Prlic, Francisco S. Domingues, and ManfORANGE J. Sippl (2000)
  Structure-derived substitution matrices for alignment of distantly related sequences
  Protein Eng. 13: 545-550
  Original similarity matrix

• Burkhard Rost (1999)
  Twilight zone of protein sequence alignments
  Protein Eng. 12: 85-94
  Pairwise sequence comparison

• Leszek Rychlewski, Lukasz Jaroszewski, Weizhong Li, and Adam Godzik (2000)
  Comparison of sequence profiles. Strategies for structural predictions using sequence information.
  Protein Sci. 9: 232-241
  Multiple profile-profile sequence comparison (FFAS03)

• Ruslan I. Sadreyev, David Baker, and Nick V. Grishin (2003)
  Profile-profile comparisons by COMPASS predict intricate homologies between protein families
  Protein Sci. 12: 2262-2272
  Multiple profile-profile sequence comparison (COMPASS)

• Ruslan I. Sadreyev and Nick V. Grishin (2003)
  COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
  J. Mol. Biol. 326: 317-336
  Multiple profile-profile sequence comparison (COMPASS)

• T.D. Schneider and R.M. Stephens (1990)
  Sequence logos: a new way to display consensus sequences
  Nucleic Acids Res. 18: 6097-6100
  Sequence logos

• V.A. Simossis and J. Heringa (2005)
  PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information
  Nucleic Acids Res. 33: W289-W294
  Multiple sequence comparison (PRALINE)

• V.A. Simossis, J. Kleinjung, and J. Heringa (2005)
  Homology-extended sequence alignment
  Nucleic Acids Res. 33: 816-824
  Multiple profile-profile sequence comparison

• R.F. Smith and T.F. Smith (1992)
  Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modelling
  Protein Eng. 5: 35-41
  Multiple sequence comparison (PIMA)

• T.F. Smith and M.S. Waterman (1981)
  Identification of common molecular sub-sequences
  J. Mol. Biol. 147: 195-197
  Pairwise sequence comparison

• Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, and Burkhard Morgenstern (2005)
  DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment
  BMC Bioinformatics 6: 66
  Multiple sequence comparison (DIALIGN-T)

• Tatiana A. Tatusova and Thomas L. Madden (1999)
  BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
  FEMS Microbiol. Lett. 174: 247-250
  Pairwise sequence comparison (BLAST 2)

• J.D. Thompson, D.G. Higgins, and T.J. Gibson (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
  Multiple sequence comparison (Clustal)

• J.D. Thompson, T.J. Gibson, F. Plewniak, F. Jeanmougin, and D.G. Higgins (1997)
  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
  Nucleic Acids Res. 25: 4876-4882
  Multiple sequence comparison (Clustal)

• Julie D. Thompson, Frédéric Plewniak, and Olivier Poch (1999)
  BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs
  Bioinformatics 15: 87-88
  Comparison of algorithms for multiple sequence comparisons

• Julie D. Thompson, Frédéric Plewniak, and Olivier Poch (1999)
  A comprehensive comparison of multiple sequence alignment programs
  Nucleic Acids Res. 27: 2682-2690
  Comparison of algorithms for multiple sequence comparisons

• J.D. Thompson, F. Plewniak, J.C. Thierry, and O. Poch (2000)
  DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches
  Nucleic Acids Res. 28: 2919-2926
  Multiple sequence comparison (DbClustal)

• Kentaro Tomii and Minoru Kanehisa (1996)
  Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins
  Protein Eng. 9: 27-36
  Comparison of similarity matrices

• Martin Vingron and Michael S. Waterman (1994)
  Sequence alignment and penalty choice. Review of concepts, case studies and implications
  J. Mol. Biol. 235: 1-12
  Comparison of similarity matrices; Role of the Gap Penalty

• Gerhard Vogt, Thure Etzold, and Patrick Argos (1995)
  An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited
  J. Mol. Biol. 249: 816-831
  Comparison of similarity matrices

• Iain M. Wallace, Gordon Blackshields, and Desmond G. Higgins
  Multiple sequence alignments
  Curr. Opin. Struct. Biol. 15: 261-266
  Multiple sequence comparison (Review)

• Guoli Wang and Roland L. Dunbrack Jr. (2004)
  Scoring profile-to-profile sequence alignments
  Protein Sci. 13: 1612-1626
  Multiple profile-profile sequence comparison

• G. Yona and M. Levitt (2002)
  Within the twilight zone: a sensitive profile-profile comparison tool based on information theory
  J. Mol. Biol. 315: 1257-1275
  Multiple profile-profile sequence comparison

Latest update of content: October 10, 2005

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