Recent developments in the MAFFT multiple sequence alignment program

Keywords

Scalability, Computer science, Consistency (knowledge bases), Multiple sequence alignment, Software

References

• A Collection of Amino Acid Replacement Matrices Derived from Clusters of Orthologs正志 花井 — 2005
• MUSCLE: a multiple sequence alignment method with reduced time and space complexityR. C. Edgar — 2004
• A strategy for the rapid multiple alignment of protein sequences. Confidence levels from tertiary structure comparisons.Geoffrey J. Barton, Michael J.E. Sternberg — 1987
• MACSIMS : multiple alignment of complete sequences information management systemJulie Thompson, Arnaud Muller, Andrew Waterhouse — 2006
• Kalign – an accurate and fast multiple sequence alignment algorithmTimo Lassmann, Erik L. L. Sonnhammer — 2005
• DIALIGN-T: An improved algorithm for segment-based multiple sequence alignmentAmarendran R Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann — 2005
• The accuracy of several multiple sequence alignment programs for proteinsPaulo Nuin, Zhouzhi Wang, Elisabeth R.M. Tillier — 2006
• GASH: An improved algorithm for maximizing the number of equivalent residues between two protein structuresDaron M. Standley, Hiroyuki Toh, Haruki Nakamura — 2005
• Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap costShinsuke Yamada, Osamu Gotoh, Hayato Yamana — 2006
• Multiple sequence alignment for phylogenetic purposesDavid A. Morrison — 2006
• A statistical score for assessing the quality of multiple sequence alignmentsVirpi Ahola, Tero Aittokallio, Mauno Vihinen — 2006
• A fast and sensitive multiple sequence alignment algorithmMartin Vingron, Patrick Argos — 1989
• Progressive sequence alignment as a prerequisitetto correct phylogenetic treesDa-Fei Feng, Russell F. Doolittle — 2007
• The multiple sequence alignment problem in biologyHumberto Carrillo-Calvet, David J. Lipman — 1988
• Protein structure alignment.William R. Taylor, Christine Orengo — 1989
• The equilibrium partition function and base pair binding probabilities for RNA secondary structureJohn S. McCaskill — 1990
• DIALIGN2: Improvement of the segment to segment approach to multiple sequence alignmentBurkhard Morgenstern — 1999
• Mauve: multiple alignment of conserved genomic sequence with rearrangements.Aaron E. Darling, Bob Mau, Frederick R. Blattner — 2004
• The alignment of sets of sequences and the construction of phyletic trees: An integrated methodPaulien Hogeweg, B. Hesper — 2005
• A tool for multiple sequence alignment.David J. Lipman, Stephen F. Altschul, John Kececioglu — 1989

Cited by

• Jaminaea angkorensis gen. nov., sp. nov., a novel anamorphic fungus containing an S943 nuclear small-subunit rRNA group IB intron represents a basal branch of Microstromatales.James D. Spinhirne, Stephen P. Palm, Dennis L. Hlavka — 2009
• Critical lysine residues within the overlooked N-terminal domain of human APE1 regulate its biological functionsR. Tzveova, T. Yaneva, George Dimitrov — 2010
• Genomic Differentiation Between Temperate and Tropical Australian Populations of Drosophila melanogasterKrystallin Hernandez — 2011
• Eight new Leptographium species associated with tree-infesting bark beetles in ChinaWinarno Surachmad — 2010
• Vanishing native American dog lineagesT. D. Barnes — 2011
• DEALING WITH INCOMPLETE TAXON SAMPLING AND DIVERSIFICATION OF A LARGE CLADE OF MUSHROOM‐FORMING FUNGI邦彦 門野, 康仁 田中 — 2011
• Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.Israel Moreno‐Contreras, Martha Cristina Arteaga Luna, Eduardo Escudero González — 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
• Structural basis for substrate targeting and catalysis by fungal polysaccharide monooxygenasesPing-Sheng Tseng — 2012
• The evolution of catalytic residues and enzyme mechanism within the bacterial nucleoside phosphorylase superfamily 1.Isidro G. Bango Torviso — 2012
• Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods達二 鵜野, 健二郎 神原, 淸吉 渡邊 — 2013
• Arthropod Phylogenetics in Light of Three Novel Millipede (Myriapoda: Diplopoda) Mitochondrial Genomes with Comments on the Appropriateness of Mitochondrial Genome Sequence Data for Inferring Deep Level RelationshipsMichael S. Brewer, Lynn Swafford, Chad L. Spruill — 2013
• Characterization of an insect-specific flavivirus (OCFVPT) co-isolated from Ochlerotatus caspius collected in southern Portugal along with a putative new Negev-like virusM.R. Gangadhar, K. Rajasekhara Reddy — 2013
• Molecular phylogenetics of Gobioidei and phylogenetic placement of European gobies.C N Paramasivan — 2013
• A phylogenetic overview of the antrodia clade (Basidiomycota, Polyporales)P. T. Stiko — 2013
• The Rediscovery of a Long Described Species Reveals Additional Complexity in Speciation Patterns of Poeciliid Fishes in Sulfide SpringsЛ. В. Автономова, Сергей Александрович Назаренко — 2013
• Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1J.M. Cacho-Blecua — 2013
• Assessment of the efficiency of in situ bioremediation techniques in a creosote polluted soil: change in bacterial community.H. Messel, David F. Crawford — 2013
• Bacteriophage T5 encodes a homolog of the eukaryotic transcription coactivator PC4 implicated in recombination-dependent DNA replication.Teguh Pudjo Muljono — 2013
• Plant homeodomain-leucine zipper I transcription factors exhibit different functional AHA motifs that selectively interact with TBP or/and TFIIBGian Luca Potestà — 2014

Related papers

• Recovering accuracy methods for scalable consistency libraryJordi Lladós, Fernando Guirado, Fernando Cores — 2015
• Alignment of protein sequences by their profilesMarc A. Martı́-Renom, M. S. Madhusudhan, Andrej Šali — 2004
• 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
• High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment toolsMiquel Orobitg, Fernando Guirado, Fernando Cores — 2015
• INTERALIGN: interactive alignment editor for distantly related protein sequencesOlivier Pible, G. Imbert, Jean‐Luc Pellequer — 2005
• ReformAlign: improved multiple sequence alignments using a profile-based meta-alignment approachDimitrios P. Lyras, Dirk Metzler — 2014
• ALIGN_MTX - An optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignmentBoris Vishnepolsky, Malak Pirtskhalava — 2009
• Grammar-based distance in progressive multiple sequence alignmentDavid J. Russell, Hasan H. Otu, Khalid Sayood — 2008