next-generation and genomic phylogenetics
Currently, I am working on methods for assembling large datasets with an emphasis on both large numbers of taxa (mega-phylogenies) and with large numbers of genes (supermatrices). I have an interest in showing how large phylogenies can illuminate problems that we have not been able to address adequately with smaller phylogenies. Until recently, I have focused on building phylogenies that have large numbers of tips but have started to explore building datasets with 454 and Illumina sequences.
Although these analyses and tools are in their infancy, preliminary results are promising and provide tools from de novo assembly of the data to the construction of the dataset.
Relevant publications
- Smith, S. A. and M. J. Donoghue. 2008. Rates of Molecular Evolution are Linked to Life History in Flowering Plants. Science. pdf
- Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics. 24: 715-716. pdf
- Smith, S. A. et al. 2008. Bioactive endophytes warrant intensified exploration and conservation. PLoS ONE. 3: e3052. pdf
- Smith, S. A., J. Beaulieu, and M. J. Donoghue. 2009. Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches. BMC Evol. Biol. link
- Dunn, C. W., A. Hejnol, D. Q. Matus, K. Pang, W. E. Browne, S. A. Smith, et al. 2008. Broad taxon sampling improves resolution of the Animal Tree of Life in phylogenomic analyses. Nature. 452: 745-749. pdf
Software
Currently, I am working on methods for assembling large datasets with an emphasis on both large numbers of taxa (mega-phylogenies) and with large numbers of genes (supermatrices). I have an interest in showing how large phylogenies can illuminate problems that we have not been able to address adequately with smaller phylogenies. Until recently, I have focused on building phylogenies that have large numbers of tips but have started to explore building datasets with 454 and Illumina sequences.
Although these analyses and tools are in their infancy, preliminary results are promising and provide tools from de novo assembly of the data to the construction of the dataset.
Relevant publications
