Method
Inferring genome-scale rearrangement phylogeny and ancestral gene order: a Drosophila case study
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* Corresponding author: Arjun Bhutkar arjunb@morgan.harvard.edu
1 BioMolecular Engineering Research Center, Boston University, Cummington St, Boston, MA 02215, USA
2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 021383, USA
Genome Biology 2007, 8:R236 doi:10.1186/gb-2007-8-11-r236
Published: 8 November 2007Additional files
Additional data file 1:
Filtered list of genes common to all Drosophila species in set (high confidence placements).
Format: TXT Size: 75KB Download file
Additional data file 2:
NGPs based on common gene set (in file 1) with arm indexing and only within Drosophila species (without outgroup pairs) - used in clustering of fly species (Figure 1a).
Format: TXT Size: 310KB Download file
Additional data file 3:
NGPs without arm indexing (to allow for NGPs from outgroup species with varying chromosome architecture) based on Drosophila common gene set (in file 1) - used in the rearrangement and ancestral gene order analysis.
Format: TXT Size: 576KB Download file
Additional data file 6:
Ancestral adjacencies (blocks) at the Drosophila root under criterion 1
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Additional data file 7:
Ancestral adjacencies (blocks) at the Drosophila root under criterion 2.
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Additional data file 8:
Summary of results of testing with the mitochondrial test dataset.
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Additional data file 9:
Tree file from PHYLIP version 3.65 for SRP54 and SRP19 gene sequences used for Figure 2.
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Additional data file 10:
Detailed description of the method.
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