From The Cover: An algorithm for progressive multiple alignment of sequences with

Keywords

Pairwise comparison, Dynamic programming, Algorithm, Multiple sequence alignment, Computer science

References

• MUSCLE: a multiple sequence alignment method with reduced time and space complexityR. C. Edgar — 2004
• Biological sequence analysisTerence P. Speed — 2003
• The alignment of sets of sequences and the construction of phyletic trees: An integrated methodPaulien Hogeweg, B. Hesper — 2005
• Dating of the human-ape splitting by a molecular clock of mitochondrial DNAMasami Hasegawa, Hirohisa Kishino, Taka-aki Yano — 2005
• An improved algorithm for matching biological sequences.Osamu Gotoh — 1982
• A general method applicable to the search for similarities in the amino acid sequence of two proteins.Saul B. Needleman, Christian D. Wunsch — 1970
• Evolutionary trees from DNA sequences: A maximum likelihood approachJoseph Felsenstein — 2005
• A workbench for multiple alignment construction and analysisGregory D. Schuler, Stephen F. Altschul, David J. Lipman — 1991
• 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
• Optimal alignments in linear spaceEugene W. Myers, Webb Miller — 1988
• The early introduction of dynamic programming into computational biologyDavid Sankoff — 2000
• MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.Kazutaka Katoh — 2002
• Profile hidden Markov modelsSean R. Eddy — 1998
• Molecular phylogenetics: state-of-the-art methods for looking into the past.Simon Whelan, Píetro Lió, Nick Goldman — 2001
• A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given.Jotun Hein — 1989
• Algorithm Theory — SWAT'96SWAT 1996 Reykjavík, Karlsson, Rolf, Lingas, Andrzej — 1996
• ProteinsJames L’Italien — 1987
• Mammalian protein metabolismH. Munro, J. B. Allison — 1964
• BMC BioinformaticsCasper J. Albers, Ritsert C. Jansen, Jan Kok — 2006

Cited by

• The Evolution of the Glucosinolate Pathway in the BrassicaceaeCarrie Olson-Manning — 2013
• Exploring the evolution of social behaviour using genomic dataAarti Venkat — 2011
• Genetic divergence and speciation in lowland and montane peruvian poison frogs.Hannes Gutzer, Jürgen Müller — 2006
• Finding regulatory elements and regulatory motifs: a general probabilistic frameworkMichael P. Hoffmann — 2007
• The heptad repeat region is a major selection target in MERS-CoV and related coronavirusesRaffaella Iafrate, Cristina Giuliani — 2015
• Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C BetacoronavirusesЛуков Валерий Андреевич, Юдин Борис Григорьевич — 2016
• Transcriptome analysis explores genes related to shikonin biosynthesis in Lithospermeae plants and provides insights into Boraginales’ evolutionary historyFrankEnderle — 2017
• Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza淳一 藤田 — 2018
• The Antarctic sea ice alga Chlamydomonas sp. ICE-L provides insights into adaptive patterns of chloroplast evolutionPeter Conradsson — 2018
• Molecular footprints of inshore aquatic adaptation in Indo-Pacific humpback dolphin (Sousa chinensis).В. А. Мерзляков, М. С. Алексеева, Р. Ю. Газизулин — 2019
• Phylogeny of the millipede order Spirobolida (Arthropoda: Diplopoda: Helminthomorpha)José Orlandis Rovira — 2010
• RNA-Alignments und RNA-Struktur in silicoAndreas Wilm — 2006
• DNA +Pro : an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein SequencesXiaolong Wang, Shuang-yong Xu, Deming Gou — 2010
• Bayesian structural phylogeneticsChristopher Challis — 2013
• Evolution of the Phosphatase Gene Family Across Nematode Worms and FliesPaulina Tsai, Melissa A. Wilson Sayres — 2013
• Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)Yingbo Niu, Jingjie Hu, Xiaolong Wang — 2011
• The Path of the Blind Watchmaker: A Model of EvolutionDavid A. Patterson, Andrew Anthony Poggio — 2011
• Phylogeny-aware alignment with PRANK.Ari Löytynoja — 2014
• Nuevas metodologías para el estudio de virus humanos contaminantes del medio ambienteCalgua de León, Byron Tomas — 2013
• Phylogénie, éléments transposables et évolution de la taille des génomes chez les lupinsFrédéric Mahé — 2009

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
• Homology-extended sequence alignmentV. A. Simossis — 2005
• Multiple sequence alignment by a pairwise algorithmWilliam R. Taylor — 1987
• Building multiple alignments from pairwise alignmentsWebb Miller — 1993
• Pairwise Sequence Alignment for Very Long Sequences on GPUsJunjie Li, Sanjay Ranka, Sartaj Sahni — 2012
• Multiple Sequence Alignment Containing a Sequence of Regular ExpressionsAbdullah N. Arslan — 2005