TCS: A web server for multiple sequence alignment evaluation and phylogenetic reconstruction

Nucleic Acids Research

Volumn 43, Issue W1, 2015, Pages W3-W6

  Chang, Jia Ming ^a,b,c   Di Tommaso, Paolo ^a,b   Lefort, Vincent ^d   Gascuel, Olivier ^d   Notredame, Cedric ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c INSTITUTE OF HUMAN GENETICS   (France)

^d UNIV MONTPELLIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLIENT SERVER APPLICATION; DATA PROCESSING; INTERNET; MEASUREMENT ACCURACY; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; TRANSITIVE CONSISTENCY SCORE WEB SERVER; WEB BROWSER; COMPUTER PROGRAM; PROCEDURES; SEQUENCE ANALYSIS;

ALGORITHMS; INTERNET; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 84979856663     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv310     Document Type: Article

References (15)

1. Chang, J.M., Di Tommaso, P. and Notredame, C. (2014) TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction. Mol. Biol. Evol., 31, 1625-1637.
2. Guindon, S., Dufayard, J.F., Lefort, V., Anisimova, M., Hordijk, W. and Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol., 59, 307-321.
3. Kemena, C. and Notredame, C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
4. Wallace, I.M., O'Sullivan, O., Higgins, D.G. and Notredame, C. (2006) M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res., 34, 1692-1699.
5. Talavera, G. and Castresana, J. (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol., 56, 564-577.
6. Capella-Gutierrez, S., Silla-Martinez, J.M. and Gabaldon, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25, 1972-1973.
7. Liu, K., Raghavan, S., Nelesen, S., Linder, C.R. and Warnow, T. (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science, 324, 1561-1564.
8. Landan, G. and Graur, D. (2007) Heads or tails: a simple reliability check for multiple sequence alignments. Mol. Biol. Evol., 24, 1380-1383.
9. Penn, O., Privman, E., Landan, G., Graur, D. and Pupko, T. (2010) An alignment confidence score capturing robustness to guide tree uncertainty. Mol. Biol. Evol., 27, 1759-1767.
10. Kim, J. and Ma, J. (2011) PSAR: measuring multiple sequence alignment reliability by probabilistic sampling. Nucleic Acids Res., 39, 6359-6368.
11. Do, C.B., Mahabhashyam, M.S., Brudno, M. and Batzoglou, S. (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
12. Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res., 30, 3059-3066.
13. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.
14. Lassmann, T. and Sonnhammer, E.L. (2005) Kalign-an accurate and fast multiple sequence alignment algorithm. BMC bioinformatics, 6, 298.
15. Flicek, P., Aken, B.L., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S. et al. (2010) Ensembl's 10th year. Nucleic Acids Res., 38, D557-D562.