primers4clades

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primers4clades (primers for clades) is developed and maintained by Pablo Vinuesa at CCG/UNAM (Mexico) and Bruno Contreras-Moreira at EEAD/CSIC (Spain), with technical support provided by Romualdo Zayas-Laguna and Victor del Moral. This project is funded by grant DGAPA IN201806-2 from DGAPA/PAPIIT-UNAM, grant P1-60071 from CONACyT-Mexico, ARAID and by grant 200720I038 from CSIC. If you use this resource we ask you to cite the main paper describing this work:

The server relies on several resources: CODEHOP, MUSCLE, Codon Usage Database, TREE-PUZZLE, PhyML, PHYLIP, Amplicon, NJplot and Bioperl.

You should cite the following references to give them credit:

1.  Anisimova, M. and Gascuel, O. (2006) Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol., 55, 539-352.

2. Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res., 32, 1792-1797.

3. Felsenstein, J. (2004). PHYLIP (Phylogeny Inference Package) v3.6. Distributed by the author. Department of Genetics, University of Washington, Seattle.

4. Guindon, S. and Gascuel, O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.

5. Jarman, S.N. (2004) Amplicon: software for designing PCR primers on aligned DNA sequences. Bioinformatics, 20, 1644-1645.

6. Rose, T.M., Henikoff, J.G. and Henikoff, S. (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res., 31, 3763-3766.

7. Rose, T.M., Schultz, E.R., Henikoff, J.G., Pietrokovski, S., McCallum, C.M. and Henikoff, S. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res., 26, 1628-1635.

8. Schmidt, H.A., Strimmer, K., Vingron, M. and von Haeseler, A. (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics, 18, 502-504.

9. 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.

This service is available AS IS and at your own risk. CCG/UNAM and EEAD/CSIC do not give any representation or warranty nor assume any liability or responsibility for the service or the results posted (whether as to their accuracy, completeness, quality or otherwise). Access to the service is available free of charge for ordinary use in the course of research. The service must not be used for direct commercial gain. We reserve the right to withdraw the service to abusing users.