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Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics

Indra Neil Sarkar1*, Mary G Egan2, Gloria Coruzzi3, Ernest K Lee4 and Rob DeSalle4

Author Affiliations

1 MBLWHOI Library, Marine Biological Laboratory, Woods Hole, MA, USA

2 Department of Biology and Molecular Biology, Montclair State University, Montclair, NJ, USA

3 Department of Biology, New York University, New York NY, USA

4 Sackler Institute for Comparative Genomics, American Museum of Natural History, New York NY, USA

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BMC Bioinformatics 2008, 9:103  doi:10.1186/1471-2105-9-103

Published: 19 February 2008

Abstract

Background

The availability of sequences from whole genomes to reconstruct the tree of life has the potential to enable the development of phylogenomic hypotheses in ways that have not been before possible. A significant bottleneck in the analysis of genomic-scale views of the tree of life is the time required for manual curation of genomic data into multi-gene phylogenetic matrices.

Results

To keep pace with the exponentially growing volume of molecular data in the genomic era, we have developed an automated technique, ASAP (Automated Simultaneous Analysis Phylogenetics), to assemble these multigene/multi species matrices and to evaluate the significance of individual genes within the context of a given phylogenetic hypothesis.

Conclusion

Applications of ASAP may enable scientists to re-evaluate species relationships and to develop new phylogenomic hypotheses based on genome-scale data.