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Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Tan, Ge ; Gil, Manuel ; Löytynoja, Ari P ; Goldman, Nick ; Dessimoz, Christophe

Proceedings of the National Academy of Sciences of the United States of America, 13 January 2015, Vol.112(2), pp.E99-100 [Peer Reviewed Journal]

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Evolution. Uniting alignments and trees

Löytynoja, Ari ; Goldman, Nick

Science (New York, N.Y.), 19 June 2009, Vol.324(5934), pp.1528-9 [Peer Reviewed Journal]

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Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

Löytynoja, Ari ; Goldman, Nick

Science (New York, N.Y.), 20 June 2008, Vol.320(5883), pp.1632-5 [Peer Reviewed Journal]

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An algorithm for progressive multiple alignment of sequences with insertions

Loeytynoja, Ari ; Goldman, Nick Loeytynoja, Ari (correspondence author)

Proceedings of the National Academy of Sciences, USA, Jul 2005, Vol.102(30), pp.10557-10562 [Peer Reviewed Journal]

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An Algorithm for Progressive Multiple Alignment of Sequences with Insertions

Löytynoja, Ari ; Goldman, Nick ; Siegmund, David O.

Proceedings of the National Academy of Sciences of the United States of America, 26 July 2005, Vol.102(30), pp.10557-10562 [Peer Reviewed Journal]

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webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

Löytynoja, Ari ; Goldman, Nick

BMC Bioinformatics, 2010, p.579 [Peer Reviewed Journal]

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Molecular Phylogenetic Analyses of the Mitochondrial ADP-ATP Carriers: The Plantae/Fungi/Metazoa Trichotomy Revisited

Löytynoja, Ari ; Milinkovitch, Michel C.

Proceedings of the National Academy of Sciences of the United States of America, 28 August 2001, Vol.98(18), pp.10202-10207 [Peer Reviewed Journal]

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Short template switch events explain mutation clusters in the human genome

Löytynoja, Ari ; Goldman, Nick

Genome research, June 2017, Vol.27(6), pp.1039-1049 [Peer Reviewed Journal]

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A model of evolution and structure for multiple sequence alignment

Löytynoja, Ari ; Goldman, Nick

Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 27 December 2008, Vol.363(1512), pp.3913-9 [Peer Reviewed Journal]

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Cleavage of the Drosophila screw prodomain is critical for a dynamic BMP morphogen gradient in embryogenesis

Künnapuu, Jaana ; Tauscher, Petra M ; Tiusanen, Nina ; Nguyen, Minh ; Löytynoja, Ari ; Arora, Kavita ; Shimmi, Osamu

Developmental Biology, 15 May 2014, Vol.389(2), pp.149-159 [Peer Reviewed Journal]

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