ALTER: Program-oriented conversion of DNA and protein alignments

Nucleic Acids Research

Volumn 38, Issue SUPPL. 2, 2010, Pages

  Glez Peña, Daniel ^a   Gómez Blanco, Daniel ^a   Reboiro Jato, Miguel ^a   Fdez Riverola, Florentino ^a   Posada, David ^a  

^a UNIVERSITY OF VIGO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; CLIENT SERVER APPLICATION; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; MOLECULAR EVOLUTION; MOLECULAR PHYLOGENY; POPULATION GENETICS; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; WEB BROWSER; INTERNET; PROCEDURES; SEQUENCE ANALYSIS;

INTERNET; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 77954321059     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq321     Document Type: Article

References (26)

1. Posada, D. (ed.), (2009) Bioinformatics for DNA sequence analysis. Humana Press, New York, NY, USA.
2. Kemena, C. and Notredame, C. (2009) Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics, 25, 2455-2465.
3. 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.
4. Gouy, M., Guindon, S. and Gascuel, O. (2010) SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol., 27, 221-224.
5. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R. et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.
6. Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B. et al. (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423.
7. Stajich, J.E., Block, D., Boulez, K., Brenner, S.E., Chervitz, S.A., Dagdigian, C., Fuellen, G., Gilbert, J.G., Korf, I., Lapp, H. et al. (2002) The Bioperl toolkit: perl modules for the life sciences. Genome Res., 12, 1611-1618.
8. Yang, Z. (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol., 24, 1586-1591.
9. Metsker, S.J. (2001) Building Parsers With Java. Addison-Wesley Professional, Boston, MA, USA.
10. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
11. Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
12. Notredame, C., Higgins, D.G. and Heringa, J. (2000) T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol., 302, 205-217.
13. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
14. Do, C.B., Mahabhashyam, M.S., Brudno, M. and Batzoglou, S. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
15. Castresana, J. (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol., 17, 540-552.
16. Hall, T.A. (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser., 41, 95-98.
17. Posada, D. (2008) jModelTest: phylogenetic model averaging. Mol. Biol. Evol., 25, 1253-1256.
18. Abascal, F., Zardoya, R. and Posada, D. (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics, 21, 2104-2105.
19. Tamura, K., Dudley, J., Nei, M. and Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol., 24, 1596-1599.
20. Ronquist, F. and Huelsenbeck, J.P. (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
21. Swofford, D.L. (2000) PAUP: Phylogenetic analysis using parsimony (and Other Methods), Sunderland, MA, USA.
22. Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.
23. Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics, 22, 2688-2690.
24. Huson, D.H. (1998) SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics, 14, 68-73.
25. Clement, M., Posada, D. and Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Mol. Ecol., 9, 1657-1659.
26. Librado, P. and Rozas, J. (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452.