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Results: 1 to 20 of 140

1.

GUIDANCE: a web server for assessing alignment confidence scores.

Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W23-8. doi: 10.1093/nar/gkq443. Epub 2010 May 23.

PMID:
20497997
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

An alignment confidence score capturing robustness to guide tree uncertainty.

Penn O, Privman E, Landan G, Graur D, Pupko T.

Mol Biol Evol. 2010 Aug;27(8):1759-67. doi: 10.1093/molbev/msq066. Epub 2010 Mar 5.

PMID:
20207713
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.

Hagopian R, Davidson JR, Datta RS, Samad B, Jarvis GR, Sjölander K.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W29-34. doi: 10.1093/nar/gkq298. Epub 2010 Apr 29.

PMID:
20430824
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.

Suyama M, Torrents D, Bork P.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W609-12.

PMID:
16845082
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

SALIGN: a web server for alignment of multiple protein sequences and structures.

Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.

PMID:
22618536
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

The PRALINE online server: optimising progressive multiple alignment on the web.

Simossis VA, Heringa J.

Comput Biol Chem. 2003 Oct;27(4-5):511-9.

PMID:
14642759
[PubMed - indexed for MEDLINE]
7.

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

Löytynoja A, Goldman N.

BMC Bioinformatics. 2010 Nov 26;11:579. doi: 10.1186/1471-2105-11-579.

PMID:
21110866
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments.

Poirot O, O'Toole E, Notredame C.

Nucleic Acids Res. 2003 Jul 1;31(13):3503-6.

PMID:
12824354
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

FFAS03: a server for profile--profile sequence alignments.

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8.

PMID:
15980471
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

FastML: a web server for probabilistic reconstruction of ancestral sequences.

Ashkenazy H, Penn O, Doron-Faigenboim A, Cohen O, Cannarozzi G, Zomer O, Pupko T.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W580-4. doi: 10.1093/nar/gks498. Epub 2012 May 31.

PMID:
22661579
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

PROMALS web server for accurate multiple protein sequence alignments.

Pei J, Kim BH, Tang M, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.

PMID:
17452345
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment.

Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W37-40.

PMID:
15215345
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.

Kuraku S, Zmasek CM, Nishimura O, Katoh K.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W22-8. doi: 10.1093/nar/gkt389. Epub 2013 May 15.

PMID:
23677614
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

MuSiC: a tool for multiple sequence alignment with constraints.

Tsai YT, Huang YP, Yu CT, Lu CL.

Bioinformatics. 2004 Sep 22;20(14):2309-11. Epub 2004 Apr 1.

PMID:
15059840
[PubMed - indexed for MEDLINE]
Free Article
15.

R-Coffee: a web server for accurately aligning noncoding RNA sequences.

Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W10-3. doi: 10.1093/nar/gkn278. Epub 2008 May 15.

PMID:
18483080
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

PROMALS3D web server for accurate multiple protein sequence and structure alignments.

Pei J, Tang M, Grishin NV.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W30-4. doi: 10.1093/nar/gkn322. Epub 2008 May 24.

PMID:
18503087
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

MultiPipMaker: comparative alignment server for multiple DNA sequences.

Elnitski L, Riemer C, Burhans R, Hardison R, Miller W.

Curr Protoc Bioinformatics. 2005 Apr;Chapter 10:Unit10.4. doi: 10.1002/0471250953.bi1004s9.

PMID:
18428743
[PubMed - indexed for MEDLINE]
18.

PicXAA-Web: a web-based platform for non-progressive maximum expected accuracy alignment of multiple biological sequences.

Sahraeian SM, Yoon BJ.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W8-12. doi: 10.1093/nar/gkr244. Epub 2011 Apr 22.

PMID:
21515632
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

TreeDet: a web server to explore sequence space.

Carro A, Tress M, de Juan D, Pazos F, Lopez-Romero P, del Sol A, Valencia A, Rojas AM.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W110-5.

PMID:
16844971
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.

PMID:
14552658
[PubMed - indexed for MEDLINE]
Free PMC Article

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