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1
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser
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webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

Löytynoja, Ari ; Goldman, Nick

BMC bioinformatics, 2010, Vol.11 (1), p.579-579 [Peer Reviewed Journal]

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2
An Algorithm for Progressive Multiple Alignment of Sequences with Insertions
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An Algorithm for Progressive Multiple Alignment of Sequences with Insertions

Ari Löytynoja ; Nick Goldman ; David O. Siegmund

Proceedings of the National Academy of Sciences - PNAS, 2005-07-26, Vol.102 (30), p.10557-10562 [Peer Reviewed Journal]

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3
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
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Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm

Löytynoja, Ari ; Vilella, Albert J ; Goldman, Nick

Bioinformatics (Oxford, England), 2012-07-01, Vol.28 (13), p.1684-1691 [Peer Reviewed Journal]

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4
Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
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Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

Loytynoja, A ; Goldman, N

Science (American Association for the Advancement of Science), 2008, Vol.320 (5883), p.1632-1635 [Peer Reviewed Journal]

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5
A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array
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A recurrent copy number variation of the NEB triplicate region: only revealed by the targeted nemaline myopathy CGH array

Kiiski, Kirsi ; Lehtokari, Vilma-Lotta ; Löytynoja, Ari ; Ahlstén, Liina ; Laitila, Jenni ; Wallgren-Pettersson, Carina ; Pelin, Katarina

European journal of human genetics : EJHG, 2015, Vol.24 (4), p.574-580 [Peer Reviewed Journal]

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6
Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization
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Wasabi: An Integrated Platform for Evolutionary Sequence Analysis and Data Visualization

Veidenberg, Andres ; Medlar, Alan ; Löytynoja, Ari

Molecular biology and evolution, 2016, Vol.33 (4), p.1126-1130 [Peer Reviewed Journal]

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7
Séance: reference-based phylogenetic analysis for 18S rRNA studies
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Séance: reference-based phylogenetic analysis for 18S rRNA studies

Medlar, Alan ; Aivelo, Tuomas ; Löytynoja, Ari

BMC evolutionary biology, 2014-11-30, Vol.14 (1), p.235-235 [Peer Reviewed Journal]

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8
A model of evolution and structure for multiple sequence alignment
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A model of evolution and structure for multiple sequence alignment

Ari Löytynoja ; Nick Goldman

Philosophical transactions. Biological sciences, 2008-12-27, Vol.363 (1512), p.3913-3919 [Peer Reviewed Journal]

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9
MATLIGN: a motif clustering, comparison and matching tool
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MATLIGN: a motif clustering, comparison and matching tool

Kankainen, Matti ; Löytynoja, Ari

BMC bioinformatics, 2007-06-08, Vol.8 (1), p.189-189 [Peer Reviewed Journal]

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10
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
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Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Margulies, Elliott H ; Cooper, Gregory M ; Asimenos, George ; Thomas, Daryl J ; Dewey, Colin N ; Siepel, Adam ; Birney, Ewan ; Keefe, Damian ; Schwartz, Ariel S ; Hou, Minmei ; Taylor, James ; Nikolaev, Sergey ; Montoya-Burgos, Juan I ; Löytynoja, Ari ; Whelan, Simon ; Pardi, Fabio ; Massingham, Tim ; Brown, James B ; Bickel, Peter ; Holmes, Ian ; Mullikin, James C ; Ureta-Vidal, Abel ; Paten, Benedict ; Stone, Eric A ; Rosenbloom, Kate R ; Kent, W James ; Bouffard, Gerard G ; Guan, Xiaobin ; Hansen, Nancy F ; Idol, Jacquelyn R ; Maduro, Valerie V B ; Maskeri, Baishali ; McDowell, Jennifer C ; Park, Morgan ; Thomas, Pamela J ; Young, Alice C ; Blakesley, Robert W ; Muzny, Donna M ; Sodergren, Erica ; Wheeler, David A ; Worley, Kim C ; Jiang, Huaiyang ; Weinstock, George M ; Gibbs, Richard A ; Graves, Tina ; Fulton, Robert ; Mardis, Elaine R ; Wilson, Richard K ; Clamp, Michele ; Cuff, James ; Gnerre, Sante ; Jaffe, David B ; Chang, Jean L ; Lindblad-Toh, Kerstin ; Lander, Eric S ; Hinrichs, Angie ; Trumbower, Heather ; Clawson, Hiram ; Zweig, Ann ; Kuhn, Robert M ; Barber, Galt ; Harte, Rachel ; Karolchik, Donna ; Field, Matthew A ; Moore, Richard A ; Matthewson, Carrie A ; Schein, Jacqueline E ; Marra, Marco A ; Antonarakis, Stylianos E ; Batzoglou, Serafim ; Goldman, Nick ; Hardison, Ross ; Haussler, David ; Miller, Webb ; Pachter, Lior ; Green, Eric D ; Sidow, Arend

Genome research, 2007-06, Vol.17 (6), p.760-774 [Peer Reviewed Journal]

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