MAFFT version 5: improvement in accuracy of multiple sequence alignment

Keywords

Multiple sequence alignment, Benchmark (surveying), Sequence alignment, Pairwise comparison, Sequence (biology)

References

• MUSCLE: a multiple sequence alignment method with reduced time and space complexityR. C. Edgar — 2004
• Generating Benchmarks for Multiple Sequence Alignments and Phylogenic ReconstructionsJens Stoye, Dorothea Evers, Folker Meyer — 1997
• OXBench: A benchmark for evaluation of protein multiple sequence alignment accuracyGPS Raghava, Stephen M. J. Searle, Patrick C. Audley — 2003
• Progressive sequence alignment as a prerequisitetto correct phylogenetic treesDa-Fei Feng, Russell F. Doolittle — 2007
• HOMSTRAD: recent developments of the Homologous Protein Structure Alignment DatabaseLucy Stebbings — 2004
• Quality assessment of multiple alignment programsTimo Lassmann, Erik L. L. Sonnhammer — 2002
• Numerical Recipes in C++: The Art of Scientific Computing (2nd edn)1 Numerical Recipes Example Book (C++) (2nd edn)2 Numerical Recipes Multi-Language Code CD ROM with LINUX or UNIX Single-Screen License Revised Version3William H. Press, Saul A. Teukolsky, William T Vettering — 2003
• Improved tools for biological sequence comparison.William R. Pearson, David J. Lipman — 1988
• The rapid generation of mutation data matrices from protein sequencesDavid T. Jones, William R. Taylor, Janet M. Thornton — 1992
• Optimal alignment between groups of sequences and its application to multiple sequence alignmentOsamu Gotoh — 1993
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.Saul B. Needleman, Christian D. Wunsch — 1970
• A novel randomized iterative strategy for aligning multiple protein sequencesMai Berger, Peter J. Munson — 1991
• Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments.Osamu Gotoh — 1996
• CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.Julie Thompson, Desmond G. Higgins, Toby J. Gibson — 1994
• Align-m-a new algorithm for multiple alignment of highly divergent sequencesIvo Van Walle, Ignace Lasters, Lode Wyns — 2004
• Comprehensive study on iterative algorithms of multiple sequence alignmentMakoto Hirosawa, Yasushi Totoki, Masaki Hoshida — 1995
• 3DCoffee: combining protein sequences and structures within multiple sequence alignments.Órla O’Sullivan, Karsten Suhre, Chantal Abergel — 2004
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.Kazutaka Katoh — 2002
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.R. C. Edgar — 2004
• The ASTRAL Compendium in 2004John‐Marc Chandonia — 2003

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• HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold RecognitionP.H. Given, J.R. Jones — 2011
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• A Computational Study of Elongation Factor G (EFG) Duplicated Genes: Diverged Nature Underlying the Innovation on the Same Structural TemplateMatilde Mercedes Arnay de la Rosa, José A. Torres Palenzuela — 2011
• Antibiotics and translationAgata L. Starosta — 2012
• Abundance of ultramicro inversions within local alignments between human and chimpanzee genomesYuichiro Hara, Tadashi Imanishi — 2011
• Carbamoyl phosphate synthetase 1 deficiency in Italy: clinical and genetic findings in a heterogeneous cohort.Vaughan Richard Purdie — 2012
• A molecular phylogeny of thermophilic fungi.M Pizarro, F. Mazzucchelli, Ignacio Ramón García — 2012
• Resistant ticks inhibit Metarhizium infection prior to haemocoel invasion by reducing fungal viability on the cuticle surface.Dana Ment, Alice C. L. Churchill, Galina Gindin — 2012
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• Surprising results on phylogenetic tree building methods based on molecular sequencesJ. A. Martínez-Álvarez — 2012

Related papers

• PIR Pairwise Alignment - A slip up for signal peptidesSeetharaaman Balaji, Rangaswamy Kalpana, Santhosh J. Eapen — 2006
• Alignment of protein sequences by their profilesMarc A. Martı́-Renom, M. S. Madhusudhan, Andrej Šali — 2004
• Evaluation of appropriateness of the score functions used in Multiple Sequence Alignments problemHalit Ergezer, Kemal Leblebi̇ci̇oğlu — 2008
• Homology-extended sequence alignmentV. A. Simossis — 2005
• Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problemsCatherine S. Grasso, Christopher Lee — 2004
• Multiple sequence alignment by a pairwise algorithmWilliam R. Taylor — 1987
• Building multiple alignments from pairwise alignmentsWebb Miller — 1993