Lecompte O, Thompson JD, Plewniak F, Thierry J, Poch O: Multiple alignment of complete sequences (MACS) in the post-genomic era. Gene 2001, 270(1–2):17–30. 10.1016/S0378-1119(01)00461-9
Article
CAS
PubMed
Google Scholar
Do CB, Mahabhashyam MS, Brudno M, Batzoglou S: ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 2005, 15(2):330–340. [http://www.genome.org/cgi/content/abstract/15/2/330] 10.1101/gr.2821705
Article
PubMed Central
CAS
PubMed
Google Scholar
Katoh K, Kuma Ki, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucl Acids Res 2005, 33(2):511–518. [http://nar.oxfordjournals.org/cgi/content/abstract/33/2/511] 10.1093/nar/gki198
Article
PubMed Central
CAS
PubMed
Google Scholar
Lassmann T, Sonnhammer E: Kalign – an accurate and fast multiple sequence alignment algorithm. BMC Bioinformatics 2005, 6: 298. [http://www.biomedcentral.com/1471–2105/6/298] 10.1186/1471-2105-6-298
Article
PubMed Central
PubMed
Google Scholar
Wallace IM, O'Sullivan O, Higgins DG, Notredame C: M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucl Acids Res 2006, 34(6):1692–1699. [http://nar.oxfordjournals.org/cgi/content/abstract/34/6/1692] 10.1093/nar/gkl091
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson JD, Koehl P, Ripp R, Poch O: BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark. Proteins 2005, 61: 127–136. [JOURNAL ARTICLE] [JOURNAL ARTICLE] 10.1002/prot.20527
Article
CAS
PubMed
Google Scholar
Van Walle I, Lasters I, Wyns L: SABmark-a benchmark for sequence alignment that covers the entire known fold space. Bioinformatics 2005, 21(7):1267–1268. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/7/1267] 10.1093/bioinformatics/bth493
Article
CAS
PubMed
Google Scholar
Morrison D, Ellis J: Effects of nucleotide sequence alignment on phylogeny estimation: a case study of 18S rDNAs of apicomplexa. Mol Biol Evol 1997, 14(4):428–441. [http://mbe.oxfordjournals.org/cgi/content/abstract/14/4/428]
Article
CAS
PubMed
Google Scholar
Ogdenw TH, Rosenberg MS: Multiple sequence alignment accuracy and phylogenetic inference. Syst Biol 2006, 55(2):314–328. 10.1080/10635150500541730
Article
Google Scholar
Sjolander K: Phylogenomic inference of protein molecular function: advances and challenges. Bioinformatics 2004, 20(2):170–179. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/2/170] 10.1093/bioinformatics/bth021
Article
PubMed
Google Scholar
Lassmann T, Sonnhammer ELL: Automatic assessment of alignment quality. Nucl Acids Res 2005, 33(22):7120–7128. [http://nar.oxfordjournals.org/cgi/content/abstract/33/22/7120] 10.1093/nar/gki1020
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson J, Muller A, Waterhouse A, Procter J, Barton G, Plewniak F, Poch O: MACSIMS : Multiple Alignment of Complete Sequences Information Management System. BMC Bioinformatics 2006, 7: 318. [JOURNAL ARTICLE] [JOURNAL ARTICLE] 10.1186/1471-2105-7-318
Article
PubMed Central
PubMed
Google Scholar
Lassmann T, Sonnhammer ELL: Kalign, Kalignvu and Mumsa: web servers for multiple sequence alignment. Nucl Acids Res 2006, 34(2):W596–599. [http://nar.oxfordjournals.org/cgi/content/abstract/34/suppl_2/W596] 10.1093/nar/gkl191
Article
PubMed Central
CAS
PubMed
Google Scholar
Thompson J, Plewniak F, Poch O: BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 1999, 15: 87–88. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/1/87] 10.1093/bioinformatics/15.1.87
Article
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 2004, 32(5):1792–1797. [http://nar.oxfordjournals.org/cgi/content/abstract/32/5/1792] 10.1093/nar/gkh340
Article
PubMed Central
CAS
PubMed
Google Scholar
Stoye J, Evers D, Meyer F: Rose: generating sequence families. Bioinformatics 1998, 14(2):157–163. 10.1093/bioinformatics/14.2.157
Article
CAS
PubMed
Google Scholar
Lee C, Grasso C, Sharlow MF: Multiple sequence alignment using partial order graphs. Bioinformatics 2002, 18(3):452–464. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/18/3/452] 10.1093/bioinformatics/18.3.452
Article
CAS
PubMed
Google Scholar
Grasso C, Lee C: Combining partial order alignment and progressive multiple sequence alignment increases alignment speed and scalability to very large alignment problems. Bioinformatics 2004, 20(10):1546–1556. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/10/1546] 10.1093/bioinformatics/bth126
Article
CAS
PubMed
Google Scholar
Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 1994, 22(22):4673–4680. [http://nar.oxfordjournals.org/cgi/content/abstract/22/22/4673] 10.1093/nar/22.22.4673
Article
PubMed Central
CAS
PubMed
Google Scholar
Morgenstern B, Frech K, Dress A, Werner T: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 1998, 14(3):290–294. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/14/3/290] 10.1093/bioinformatics/14.3.290
Article
CAS
PubMed
Google Scholar
Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15(3):211–218. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/15/3/211] 10.1093/bioinformatics/15.3.211
Article
CAS
PubMed
Google Scholar
Katoh K, Misawa K, Kuma Ki, Miyata T: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl Acids Res 2002, 30(14):3059–3066. [http://nar.oxfordjournals.org/cgi/content/abstract/30/14/3059] 10.1093/nar/gkf436
Article
PubMed Central
CAS
PubMed
Google Scholar
Notredame C, Higgins DG, Heringa J: T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302: 205–217. 10.1006/jmbi.2000.4042
Article
CAS
PubMed
Google Scholar