References
- Altschul, S. F., Madden, T. L., Sch ffer, A. A., Zhang, J., Zhang, Z., Miller, W., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25(17), p 3389.
- Benson, D. A., Boguski, M. S., Lipman, D. J., Ostell, J., Ouellette, B. F. F., Rapp, B. A., et al. (1999) GenBank. Nucleic Acids Research 27(1), pp 12–17.
- Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2011) GenBank. Nucleic Acids Research 39, pp D32–D37.
- Bininda-Emonds, O. R. P., Cardillo, M., Jones, K. E., MacPhee, R. D. E., Beck, R. M. D., Grenyer, R., et al. (2008) The delayed rise of present-day mammals (vol 446, pg 507, 2007). Nature 456(7219), pp 274–274.
- Cavender-Bares, J., Kozak, K. H., Fine, P. V. A., & Kembel, S. W. (2009) The merging of community ecology and phylogenetic biology. Ecology Letters 12(7), pp 693–715.
- Ciccarelli, F. D., Doerks, T., Von Mering, C., Creevey, C. J., Snel, B., & Bork, P. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311(5765), p 1283.
- Edgar, R. C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1), p 113.
- Francesca D. Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J. Creevey, 1, et al. (2006) Toward Automatic Reconstruction of a Highly Resolved Tree of Life. SCIENCE 311, p 1283.
- Gao, Y., Meng, Z., He, X., Liu, Y., Zhou, Y., & Li, J. (2011) A solution to integrate data for phylogenetic research. iCBBE(1), pp 1–4.
- Goecks, J., Nekrutenko, A., Taylor, J., & Galaxy Team, T. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology 11(8), p R86.
- Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0. Systematic Biology 59(3), pp 307–321.
- Izquierdo-Carrasco, F., Smith, S. A., & Stamatakis, A. (2011) Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. BMC Bioinformatics 12(1), p 470.
- Julie D.Thompson, D. G. H. a. T. J. G. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22(22), pp 4673–4680.
- Li, C. H., Orti, G., Zhang, G., & Lu, G. Q. (2007) A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. Bmc Evolutionary Biology 7.
- Li, J., Meng, Z., Hou, Y., Zhou, Y., & Gao, Y. (2013) PartFastTree: Constructing Large Phylogenetic Trees & Estimating Their Reliability. 2013 9th International Conference on Natural Computation.
- Li, K. B. (2003) ClustalW-MPI: ClustalW analysis using distributed and parallel computing. Bioinformatics 19(12), pp 1585–1586.
- Lin, X., Meng, Z., He, X., Liu, Q., Liu, Y., Li, J., et al. (2010) A solution to integrate the phylogenetic tree’s generation based on web. iCBBE(1), pp 1–3.
- Liu, H.-M., Dyer, R. J., Guo, Z.-Y., Meng, Z., Li, J.-H., & Schneider, H. (2012) The Evolutionary Dynamics of Apomixis in Ferns: A Case Study from Polystichoid Ferns. Journal of Botany, 2012, p 11.
- McMahon, M. M., & Sanderson, M. J. (2006) Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes. Systematic Biology 55(5), pp 818–836.
- Meng, Z., Li, J., Zhou, Y., Cao, W., Xiao, X., Zhao, J., et al. (2012) GSQCT: A solution to screening gene sequences for phylogenetics analysis. 2012 9th International Conference on Fuzzy Systems and Knowledge Discovery 6, pp 2941–2945.
- Meng, Z., Li, J., Zhou, Y., Liu, Q., Liu, Y., & Cao, W. (2011) bCloudBLAST: an Efficient MapReduce Program for Bioinformatics Applications. BMEI 4, pp 2085–2089.
- Meng, Z., Lin, X., He, X., Gao, Y., Liu, H., Liu, Y., et al. (2011) Construction of the Platform for Phylogenetic Analysis. Data Driven e-Science, ISBN 978-1-4419-8013-7. Springer Science+ Business Media, LLC, pp 507–514.
- Meng, Z., Shao, J., Cao, W., Li, J., Zhou, Y., Wang, X., et al. (2014) RapidTree: a solution to rapid reconstruction phylogenetic tree. FSKD.
- Meng, Z., Xiao, X., Li, J., Zhou, Y., Cao, W., & Shen, G. (2012) Cloud-GSQCT: a parallel approach to screen gene sequences for phylogenetics analysis. 2012 International Conference on Computer Science and Information Processing, pp 660–663.
- Meng, Z., Zhou, Y., Li, J., Gao, Y., & Shen, Z. (2012) iDNABar: a rapid species identification toolbox for DNA Barcoding collection, preservation, identification and tracing. Advances in Intelligent and Soft Computing 124, pp 337–343.
- Pearse, W. D., Purvis, A., & Paradis, E. (2013) phyloGenerator: an automated phylogeny generation tool for ecologists. Methods in Ecology and Evolution 4(7), pp 692–698.
- Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) FastTree 2¨Capproximately maximum-likelihood trees for large alignments. PLoS One 5(3), p e9490.
- Ratnasingham, S., & Hebert, P. D. N. (2007) BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Molecular Ecology Notes 7(3), pp 355–364.
- Rindone, W. P. (1983) Genbank. Trends in Pharmacological Sciences 4(8), pp 326–326.
- Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Hohna, S., et al. (2012) MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology 61(3), pp 539–542.
- Sanderson, M. J., Boss, D., Chen, D., Cranston, K. A., & Wehe, A. (2008) The PhyLoTA browser: Processing GenBank for molecular phylogenetics research. Systematic Biology 57(3), pp 335–346.
- Schindel, D., & Miller, S. E. (2005) DNA barcoding a useful tool for taxonomists. Nature.
- Smith, S. A., Beaulieu, J.M., & Donoghue, M.J. (2009) Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMCEvolutionary Biology 37(9).
- Stamatakis, A. (2006) RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21), pp 2688–2690.
- Wapinski, I., Pfeffer, A., Friedman, N., & Regev, A. (2007) Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatic, 23(13), pp i549–i558.
- Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. (2002) Phylogenies and Community Ecology. Annual Review of Ecology and Systematics 33(1), pp 475–505.
- Wu, Z. Y., Lu, A. M., Tang, Y. C., Chen, Z. D., Li, D. Z. (2003) The Families and Genera of Angiosperms in China- A Comprehensive Analysis. Science Press.
- Zmasek, C. M., & Eddy, S. R. (2001) ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17, pp 383–384.