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Items: 1 to 20 of 119

1.

Phylo: a citizen science approach for improving multiple sequence alignment.

Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.

2.

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.

Kwak D, Kam A, Becerra D, Zhou Q, Hops A, Zarour E, Kam A, Sarmenta L, Blanchette M, Waldispühl J.

Genome Biol. 2013;14(10):R116.

3.
4.

SLAM web server for comparative gene finding and alignment.

Cawley S, Pachter L, Alexandersson M.

Nucleic Acids Res. 2003 Jul 1;31(13):3507-9.

5.

MAVID multiple alignment server.

Bray N, Pachter L.

Nucleic Acids Res. 2003 Jul 1;31(13):3525-6.

6.

Kalign--an accurate and fast multiple sequence alignment algorithm.

Lassmann T, Sonnhammer EL.

BMC Bioinformatics. 2005 Dec 12;6:298.

7.

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I.

Bioinformatics. 2004 Mar 22;20(5):636-43. Epub 2004 Jan 22.

PMID:
15033870
8.

CMSA: a heterogeneous CPU/GPU computing system for multiple similar RNA/DNA sequence alignment.

Chen X, Wang C, Tang S, Yu C, Zou Q.

BMC Bioinformatics. 2017 Jun 24;18(1):315. doi: 10.1186/s12859-017-1725-6.

9.

Lessons from Fraxinus, a crowd-sourced citizen science game in genomics.

Rallapalli G; Fraxinus Players, Saunders DG, Yoshida K, Edwards A, Lugo CA, Collin S, Clavijo B, Corpas M, Swarbreck D, Clark M, Downie JA, Kamoun S; Team Cooper, MacLean D.

Elife. 2015 Jul 29;4:e07460. doi: 10.7554/eLife.07460.

10.

FootPrinter3: phylogenetic footprinting in partially alignable sequences.

Fang F, Blanchette M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W617-20.

11.

CSA: an efficient algorithm to improve circular DNA multiple alignment.

Fernandes F, Pereira L, Freitas AT.

BMC Bioinformatics. 2009 Jul 23;10:230. doi: 10.1186/1471-2105-10-230.

12.

Grammar-based distance in progressive multiple sequence alignment.

Russell DJ, Otu HH, Sayood K.

BMC Bioinformatics. 2008 Jul 10;9:306. doi: 10.1186/1471-2105-9-306.

13.

MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences.

Lee BT, Tan TW, Ranganathan S.

Nucleic Acids Res. 2003 Jul 1;31(13):3533-6.

14.

Multiple alignment of DNA sequences with MAFFT.

Katoh K, Asimenos G, Toh H.

Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.

PMID:
19378139
15.

MUTAGEN: multi-user tool for annotating genomes.

Brügger K, Redder P, Skovgaard M.

Bioinformatics. 2003 Dec 12;19(18):2480-1.

PMID:
14668237
16.

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.

BMC Bioinformatics. 2006 Oct 3;7:428.

17.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

18.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

Hanson-Smith V, Johnson A.

PLoS Comput Biol. 2016 Jul 29;12(7):e1004976. doi: 10.1371/journal.pcbi.1004976. eCollection 2016 Jul.

19.

Short read alignment with populations of genomes.

Huang L, Popic V, Batzoglou S.

Bioinformatics. 2013 Jul 1;29(13):i361-70. doi: 10.1093/bioinformatics/btt215.

20.

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